WO2015113007A1 - De-immunized shiga toxin a subunit effector polypeptides for applications in mammals - Google Patents

De-immunized shiga toxin a subunit effector polypeptides for applications in mammals Download PDF

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Publication number
WO2015113007A1
WO2015113007A1 PCT/US2015/012970 US2015012970W WO2015113007A1 WO 2015113007 A1 WO2015113007 A1 WO 2015113007A1 US 2015012970 W US2015012970 W US 2015012970W WO 2015113007 A1 WO2015113007 A1 WO 2015113007A1
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WO
WIPO (PCT)
Prior art keywords
seq
shiga toxin
polypeptide
protein
toxin effector
Prior art date
Application number
PCT/US2015/012970
Other languages
French (fr)
Inventor
Eric POMA
Erin WILLERT
Garrett Lee ROBINSON
Sangeetha RAJAGOPOLAN
Brigitte BRIESCHKE
Original Assignee
Molecular Templates, Inc.
Priority date (The priority date is an assumption and is not a legal conclusion. Google has not performed a legal analysis and makes no representation as to the accuracy of the date listed.)
Filing date
Publication date
Application filed by Molecular Templates, Inc. filed Critical Molecular Templates, Inc.
Priority to IL287490A priority Critical patent/IL287490B/en
Priority to EP15704153.4A priority patent/EP3099705B1/en
Priority to JP2016546493A priority patent/JP6646584B2/en
Priority to US15/114,487 priority patent/US20160340394A1/en
Priority to IL294746A priority patent/IL294746B2/en
Priority to EP19173105.8A priority patent/EP3575312A1/en
Priority to KR1020237005041A priority patent/KR102692200B1/en
Priority to MX2016009809A priority patent/MX2016009809A/en
Priority to CN201580015672.2A priority patent/CN106414483A/en
Priority to KR1020167022292A priority patent/KR20160111951A/en
Priority to ES15704153T priority patent/ES2749862T3/en
Priority to KR1020227001129A priority patent/KR102500408B1/en
Priority to CA2937407A priority patent/CA2937407A1/en
Priority to AU2015209065A priority patent/AU2015209065C1/en
Priority to MX2016016288A priority patent/MX2016016288A/en
Priority to ES18207811T priority patent/ES2919749T3/en
Priority to IL286804A priority patent/IL286804B/en
Priority to CN202111114179.XA priority patent/CN113831416A/en
Priority to PCT/US2015/035179 priority patent/WO2015191764A1/en
Priority to KR1020177000364A priority patent/KR102496206B1/en
Priority to CA2947048A priority patent/CA2947048C/en
Priority to EP18207811.3A priority patent/EP3514168B1/en
Priority to EP21186953.2A priority patent/EP3950706A1/en
Priority to US15/317,892 priority patent/US10815469B2/en
Priority to EP15733018.4A priority patent/EP3137488B1/en
Priority to JP2016569950A priority patent/JP6735237B2/en
Priority to AU2015274647A priority patent/AU2015274647C1/en
Priority to ES15733018T priority patent/ES2717751T3/en
Priority to CN201580040778.8A priority patent/CN106604934A/en
Publication of WO2015113007A1 publication Critical patent/WO2015113007A1/en
Priority to US14/965,882 priority patent/US20160177284A1/en
Priority to IL246632A priority patent/IL246632B/en
Priority to US15/747,501 priority patent/US20210138076A2/en
Priority to IL249006A priority patent/IL249006B/en
Priority to MX2020004420A priority patent/MX2020004420A/en
Priority to US16/013,600 priority patent/US20180291359A1/en
Priority to AU2019204364A priority patent/AU2019204364C1/en
Priority to AU2019240612A priority patent/AU2019240612B2/en
Priority to IL273035A priority patent/IL273035B/en
Priority to JP2020120117A priority patent/JP7054948B2/en
Priority to US17/030,657 priority patent/US20210017512A1/en
Priority to AU2020260425A priority patent/AU2020260425B2/en
Priority to AU2020294212A priority patent/AU2020294212B2/en
Priority to US17/345,576 priority patent/US12065469B2/en
Priority to US17/459,133 priority patent/US20220401568A1/en
Priority to AU2022201220A priority patent/AU2022201220A1/en
Priority to JP2022052815A priority patent/JP2022088518A/en
Priority to AU2022256081A priority patent/AU2022256081B2/en

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Definitions

  • the present invention relates to de- immunized Shiga toxin effector polypeptides derived from A Subunits of naturally occurring Shiga toxins.
  • Polypeptides of the invention are beneficial alone or as components of molecules, e.g. therapeutics, for administration to mammals where reducing associated immune responses is desirable.
  • the polypeptides of this invention may be used as components of specifically targeted molecules, e.g. immunotoxins and ligand-toxin fusions, for the targeted killing of specific cell types.
  • Proteins of the invention have uses as, e.g., components of therapeutics and diagnostics for the diagnosis, prognosis, and treatment of a variety of diseases, disorders and conditions, including cancers, tumors, immune disorders, and microbial infections.
  • Shiga toxins have been synthetically engineered for medical applications by rational alterations to the toxin's structure, characteristics, and biological activities (see, e.g. US7713915, EP1051482, EP1727827, EP1945660;
  • Shiga toxin A Subunits are stable, enzymatically active, and cytotoxic even if truncated or fused to other protein domains (Haddad J et al, J Bacteriol 175:
  • Shiga toxin A Subunit- derived polypeptides may be linked or fused to immunoglobulin domains or receptor ligands through chemical conjugation or recombinant protein engineering in order to create cell-targeted therapeutic molecules.
  • One aim of such molecular engineering is to design chimeric molecules with the dual functionality of: 1) delivering toxins to specific cell types or places within an organism after systemic administration; and 2) effectuating a targeted cytotoxicity to specific cells using potent cytotoxic mechanisms effective in eukaryotic cells.
  • Antigenicity and/or immunogenicity results from the ability of an antigenic epitope of a molecule to induce an antibody and/or immune response when that molecule is administered in vivo.
  • Most therapeutic proteins are believed to induce an immune response of some sort, which ranges from production of low- level, low-affinity and transient antibodies like IgM to high-level, high-affinity IgG antibodies (Schellekens H, Clin Ther 24: 1720-30 (2002); Schellekens H, Nat Rev Drug Discov 1 : 457-62 (2002)).
  • Unwanted immunogenicity of a therapeutic product could result in unfavorable consequences, such as a reduced efficacy, altered pharmacokinetics, general immune and hypersensitivity reactions, anaphylaxis, and anaphylactoid reactions (Buttel I et al, Biologicals 39: 100-9 (201 1)).
  • the production of neutralizing antibodies or anti-drug antibodies in a patient can limit the long-term effectiveness of repeated doses or chronic administration of a therapeutic.
  • the immunogenic potential of a protein can be reduced by removing or disrupting epitopes likely to be recognized by the adaptive immune system.
  • Epitope disruption or removal can be accomplished by mutation, e.g. truncation, deletion, or amino acid substitution, or humanization ( agata S, Pastan I, Adv Drug Deliv Rev 61 : 977-85 (2009); Baker M et al., Self Nonself ⁇ : 314-22 (2010)).
  • B-cell B-lymphocyte
  • Activated B-cells expressing single Ig isotypes can undergo selection for those B-cells which produce antibodies with high-affinity to specific antigenic epitopes.
  • the disruption of an epitope in a therapeutic may prevent, upon administration to a subject of the therapeutic, the production of high affinity antibodies that specifically bind that epitope as well as the formation of long-lived memory B-cells targeting that epitope.
  • B-cell epitopes can be identified by various empirical methods using a combination of mutagenesis and antibodies, immunization, or phage display screening of immunoglobulin libraries. Putative B-cell epitopes can be predicted using computational tools which scan for predicted linear and discontinuous epitopes in a given polypeptide sequence which may then be disrupted in attempts to silence them (Larsen et al,
  • Epitope disruption is often attempted by mutating charged and/or aromatic residues within putative B-cell epitopes to alanine residues (Onda M et al, J Immunol 177: 8822-34 (2006); ui W Qt al, Proc Natl Acad Sci USA 109: 11782-7 (2012); Yumura K et al, Protein Sci 22: 213-21 (2012)). Furthermore, the accurate mapping and disruption of all potential epitopes, while maintaining biotherapeutic activity, may be an elusive goal for larger proteins (Brauer F et al, Antimicrob Agents Chemother 57: 678-88 (2013)).
  • Shiga toxins show promise for being engineered into useful products for therapeutic and diagnostic applications, but their potential immunogenicity may be an obstacle to uses in medical applications.
  • Shiga toxins are bacterial proteins which are highly foreign to the human immune system.
  • the antigenic and/or immunogenic sites within the A Subunits of Shiga toxins have not been systematically mapped. It would be desirable to have improved Shiga toxin A Subunit-derived polypeptides with reduced antigenicity and/or immunogenicity which retain sufficient Shiga toxin effector functions for medical applications, e.g., as components of various therapeutics involving targeted delivery of cytotoxicity to specific cell types.
  • the present invention provides Shiga toxin effector polypeptides which have reduced antigenic and/or immunogenic potential in mammals (referred to herein as "de-immunized”).
  • the present invention provides cytotoxic proteins and diagnostic proteins comprising de-immunized Shiga toxin effector polypeptides.
  • De-immunized polypeptides derived from Shiga toxin A Subunits may be linked to one or more polypeptides that mediate cell targeting via specific extracellular binding interactions to enable the engineering of improved therapeutics for cell type specific targeting of cellular internalization and Shiga toxin cytotoxicity.
  • the linking of detection promoting agents with de- immunized Shiga toxin effector region polypeptides enables the engineering of improved diagnostic molecules for detecting the presence of specific cell types.
  • the polypeptides and proteins of the invention have uses for targeted cell killing, delivering exogenous materials into specific cell types, obtaining diagnostic information, and as therapeutics for the treatment of a variety of diseases, disorders, and conditions, including cancers, immune disorders, and microbial infections.
  • a polypeptide of the invention comprises a Shiga toxin effector region comprising a polypeptide derived from the amino acid sequence of the A Subunit of at least one member of the Shiga toxin family with at least one predicted B-cell epitope removed or disrupted by mutation in such a way that at least one Shiga toxin effector function is retained.
  • Certain embodiments of the polypeptides of the invention comprise a Shiga toxin effector region comprising a polypeptide derived from the amino acid sequence of the A Subunit of at least one member of the Shiga toxin family with at least one predicted B-cell epitope removed or disrupted by mutation in such a way that at least one Shiga toxin effector function is retained; and wherein an ectopic, MHC class I-restricted, T-cell epitope is not introduced by any B-cell epitope disruption.
  • MHC class I-restricted, T-cell epitopes are known or can be predicted by the skilled worker.
  • ectopic refers to MHC class I-restricted, T-cell epitopes which are not natively present in the polypeptide before said polypeptide was de-immunized, i.e. the parental polypeptide before one or more B-cell epitope was removed and/or disrupted.
  • Certain embodiments of the invention provide polypeptides comprising a de-immunized Shiga toxin effector region comprising an amino acid sequence derived from an A Subunit of a member of the Shiga toxin Family, the Shiga toxin effector region comprising a disruption of at least one epitope region of the Shiga toxin A Subunit amino acid sequence selected from the group of natively positioned amino acid residues consisting of: 94-1 15 of SEQ ID NO: 1, SEQ ID NO:2, or SEQ ID O:3; 141-153 of SEQ ID O: l or SEQ ID O:2; 140-156 of SEQ ID O:3; 179-190 of SEQ ID O: l or SEQ ID O:2; 179-191 of SEQ ID NO:3; 204 of SEQ ID O:3; 205 of SEQ ID O: l or SEQ ID O:2; or 210-218 of SEQ ID NO:3; wherein the Shiga toxin effector region
  • Certain embodiments of the invention provide polypeptides comprising a de-immunized Shiga toxin effector region comprising an amino acid sequence derived from an A Subunit of a member of the Shiga toxin Family, the Shiga toxin effector region comprising a disruption of at least one epitope region of the Shiga toxin A Subunit amino acid sequence selected from the group of natively positioned amino acid residues consisting of: 94-1 15 of SEQ ID NO: 1, SEQ ID NO:2, or SEQ ID NO:3; 141-153 of SEQ ID NO: l or SEQ ID NO:2; 140-156 of SEQ ID NO:3; 179-190 of SEQ ID NO: l or SEQ ID NO:2; 179-191 of SEQ ID NO:3; 204 of SEQ ID NO:3; 205 of SEQ ID NO: l or SEQ ID NO:2; or 210-218 of SEQ ID NO:3; wherein the Shiga toxin effector region
  • Certain embodiments of the invention provide polypeptides comprising a de-immunized Shiga toxin effector region comprising an amino acid sequence derived from an A Subunit of a member of the Shiga toxin Family, the Shiga toxin effector region comprising a disruption of at least one epitope region of the Shiga toxin A Subunit amino acid sequence selected the group of natively positioned amino acid residues consisting of: 94-1 15 of SEQ ID NO: 1, SEQ ID NO:2, or SEQ ID O:3; 141-153 of SEQ ID O: l or SEQ ID O:2; 140-156 of SEQ ID O:3; 179-190 of SEQ ID NO: 1 or SEQ ID NO:2; 179-191 of SEQ ID NO: 3; 204 of SEQ ID NO:3; 205 of SEQ ID NO: l or SEQ ID NO :2; or 210-218 of SEQ ID NO:3; wherein the Shiga toxin effector region is
  • Certain embodiments of the invention provide polypeptides comprising a de-immunized Shiga toxin effector region comprising an amino acid sequence derived from an A Subunit of a member of the Shiga toxin Family, the Shiga toxin effector region comprising a disruption of at least one epitope region of the Shiga toxin A Subunit amino acid sequence selected from the group of natively positioned amino acid residues consisting of: 94-1 15 of SEQ ID NO: 1, SEQ ID NO:2, or SEQ ID NO:3; 141-153 of SEQ ID NO: l or SEQ ID NO:2; 140-156 of SEQ ID NO:3; 179-190 of SEQ ID NO: l or SEQ ID NO:2; 179-191 of SEQ ID NO: 3; 204 of SEQ ID NO:3; 205 of SEQ ID NO: l or SEQ ID NO :2; or 210-218 of SEQ ID NO:3; wherein the Shiga toxin effector
  • Certain embodiments of the invention provide polypeptides comprising a de-immunized Shiga toxin effector region comprising an amino acid sequence derived from an A Subunit of a member of the Shiga toxin Family, the Shiga toxin effector region comprising a disruption of at least one epitope region of the Shiga toxin A Subunit amino acid sequence selected from the group of natively positioned amino acid residues consisting of: 1-15 of SEQ ID NO: 1 or SEQ ID NO:2; 3-14 of SEQ ID NO:3; 26-37 of SEQ ID NO:3; 27-37 of SEQ ID NO: l or SEQ ID NO:2; 39-48 of SEQ ID NO: 1 or SEQ ID NO:2; 42-48 of SEQ ID NO:3; 53-66 of SEQ ID NO: l, SEQ ID NO:2, or SEQ ID NO:3; wherein the Shiga toxin effector region is capable of exhibiting a a Shiga toxin effector
  • Certain embodiments of the invention provide polypeptides comprising a de-immunized Shiga toxin effector region comprising an amino acid sequence derived from an A Subunit of a member of the Shiga toxin Family, the Shiga toxin effector region comprising a disruption of at least one epitope region of the Shiga toxin A Subunit amino acid sequence selected from the group of natively positioned amino acid residues consisting of: 1-15 of SEQ ID NO: 1 or SEQ ID NO:2; 3-14 of SEQ ID NO:3; 26-37 of SEQ ID NO:3; 27-37 of SEQ ID NO: l or SEQ ID NO:2; 39-48 of SEQ ID NO: 1 or SEQ ID NO:2; 42-48 of SEQ ID NO:3; 53-66 of SEQ ID NO: l, SEQ ID NO:2, or SEQ ID NO:3; wherein the Shiga toxin effector region is capable of exhibiting a significant level of a Shiga tox
  • Certain embodiments of the invention provide polypeptides comprising a de-immunized Shiga toxin effector region comprising an amino acid sequence derived from an A Subunit of a member of the Shiga toxin Family, the Shiga toxin effector region comprising a disruption of at least one epitope region of the Shiga toxin A Subunit amino acid sequence selected from the group of natively positioned amino acid residues consisting of: 1-15 of SEQ ID NO: 1 or SEQ ID NO:2; 3-14 of SEQ ID O:3; 26-37 of SEQ ID O:3; 27-37 of SEQ ID O: l or SEQ ID NO:2; 39-48 of SEQ ID NO: 1 or SEQ ID NO:2; 42-48 of SEQ ID NO:3; 53-66 of SEQ ID NO: l, SEQ ID NO:2, or SEQ ID NO:3; wherein the Shiga toxin effector region is capable of exhibiting a Shiga toxin effector function;
  • Certain embodiments of the invention provide polypeptides comprising a de-immunized Shiga toxin effector region comprising an amino acid sequence derived from an A Subunit of a member of the Shiga toxin Family, the Shiga toxin effector region comprising a disruption of at least one epitope region of the Shiga toxin A Subunit amino acid sequence selected from the group of natively positioned amino acid residues consisting of: 240-260 of SEQ ID NO:3; 243- 257 of SEQ ID NO: 1 or SEQ ID NO:2; 254-268 of SEQ ID NO: 1 or SEQ ID NO:2; 262-278 of SEQ ID NO:3; 281-297 of SEQ ID NO:3; and 285-293 of SEQ ID NO: 1 or SEQ ID NO:2; wherein the Shiga toxin effector region is capable of exhibiting a Shiga toxin effector function; and wherein the Shiga toxin effector region comprises no carboxy terminus
  • Certain embodiments of the invention provide polypeptides comprising a de-immunized Shiga toxin effector region comprising an amino acid sequence derived from an A Subunit of a member of the Shiga toxin Family, the Shiga toxin effector region comprising a disruption of at least one epitope region of the Shiga toxin A Subunit amino acid sequence selected from the group of natively positioned amino acid residues consisting of: 240-260 of SEQ ID NO:3; 243- 257 of SEQ ID NO: 1 or SEQ ID NO:2; 254-268 of SEQ ID NO: 1 or SEQ ID NO:2; 262-278 of SEQ ID NO:3; 281-297 of SEQ ID NO:3; and 285-293 of SEQ ID NO: 1 or SEQ ID NO:2; wherein the Shiga toxin effector region is capable of exhibiting a Shiga toxin effector function; wherein the disruption is not of a single epitope region and does not solely consist
  • the de-immunized Shiga toxin effector region polypeptide of the invention comprises an epitope disruption which comprises a deletion of at least one amino acid within an epitope region provided herein.
  • a polypeptide of the invention comprises an epitope disruption which comprises an insertion of at least one amino acid within an epitope region provided.
  • the polypeptides comprise a disruption which comprises an inversion or other rearrangement of amino acids, wherein at least one inverted amino acid is within the epitope region provided.
  • the polypeptides comprise an epitope disruption which comprises an amino acid residue mutation, such as a single amino acid substitution to a non-standard amino acid or an amino acid with a chemically modified side chain.
  • the de-immunized Shiga toxin effector regions comprise an epitope disruption which comprises an amino acid residue substitution within an epitope region provided herein.
  • the polypeptides comprise at least one substitution to an amino acid selected from the group consisting of: A, G, V, L, I, P, C, M, F, S, D, N, Q, H, and K.
  • the polypeptide comprise a substitution selected from the group consisting of: D to A, D to G, D to V, D to L, D to I, D to F, D to S, D to Q, E to A, E to G, E to V, E to L, E to I, E to F, E to S, E to Q, E to N, E to D, E to M, E to R, G to A, H to A, H to G, H to V, H to L, H to I, H to F, H to M, K to A, K to G, K to V, K to L, K to I, K to M, K to H, L to A, L to G, N to A, N to G, N to V, N to L, N to I, N to F, P to A, P to G, P to F, R to A, R to G, R to V, R to L, R to I, R to F, R to M, R to Q, R to S, R to K, R to H, S to A, S to A, S to
  • the de-immunized Shiga toxin effector regions comprise a disruption which comprises an amino acid residue substitution within an epitope region, wherein the substitution occurs at the natively positioned amino acid selected from the group of natively positioned amino acid residues consisting of: 1 of SEQ ID NO: 1 or SEQ ID NO:2; 4 of SEQ ID NO: 1, SEQ ID NO:2, or SEQ ID NO:3; 8 of SEQ ID NO:l, SEQ ID NO:2, or SEQ ID NO:3; 9 of SEQIDNO:l, SEQIDNO:2, orSEQIDNO:3; 11 of SEQ ID NO: 1, SEQ ID NO:2, or SEQ ID NO:3; 33 of SEQ ID NO:l or SEQ ID NO:2; 43 of SEQ ID NO: 1 or SEQ ID NO:2; 45 of SEQ ID NO: 1 or SEQ ID NO:2; 47 of SEQ ID NO:l or SEQ ID NO:2; 48 of SEQ ID NO:l, SEQ ID NO
  • the polypeptides comprise an epitope disruption which comprises an amino acid residue substitution within an epitope region, wherein the substitution is to any non-conservative amino acid and the substitution occurs at the amino acid residue selected from the group of natively positioned amino acid residues consisting of: 1 of SEQ ID NO: 1 or SEQ ID NO:2; 4 of SEQ ID NO:l, SEQ ID NO:2, or SEQ ID NO:3; 8 of SEQ ID NO:l, SEQ ID NO:2, or SEQ ID NO:3; 9 of SEQ ID NO:l, SEQ ID NO:2, or SEQ ID NO:3; 11 of SEQ IDNO:l, SEQ ID NO:2, or SEQ IDNO:3; 33 of SEQ ID NO:l or SEQ ID NO:2; 43 of SEQ ID NO: 1 or SEQ ID NO:2; 45 of SEQ ID NO: 1 or SEQ ID NO:2; 47 of SEQ ID NO: 1 or SEQ ID NO:2; 48 of SEQ ID NO: 1, SEQ ID NO
  • a non-conservative amino acid substitution is a substitution of one amino acid with another amino acid which has one or more markedly different biochemical properties, such as, e.g., charged to uncharged, polar to hydrophobic, and bulky to small.
  • the polypeptides comprise an epitope disruption which comprises an amino acid residue substitution within an epitope region, wherein the substitution occurs at the natively positioned amino acid residue and the substitution is to an amino acid selected from the group consisting of: Kl to A, G, V, L, I, F, M and H; T4 to A, G, V, L, I, F, M, and S; S8 to A, G, V, I, L, F, and M; T9 to A, G, V, I, L,
  • G, V, L, I, F, and M G147 to A; R179 to A, G, V, L, I, F, M, Q, S, K, and H; T180 to A, G, V, L, I, F, M, and S; T181 to A, G, V, L, I, F, M, and S; D183 to A, G, V, L, I, F, S, and Q; D184 to A, G, V, L, I, F, S, and Q; S186 to A, G, V, I, L, F, and M; G187 to A; R188 to A, G, V, L, I, F, M, Q, S, K, and H; S189 to A, G, V, I, L, F, and M; R204 to A, G, V, L, I, F, M, Q, S, K, and H; R205 to A, G, V, L, I, F, M, Q, S, K and H; S247 to A, G, V, I,
  • the polypeptides of the invention comprise the de-immunized Shiga toxin effector region derived from amino acids 75 to 251 of SEQ ID NO: 1, SEQ ID NO:2, or SEQ ID NO:3.
  • the polypeptides of the invention comprise a de-immunized Shiga toxin effector region derived from amino acids 1 to 251 of SEQ ID NO: 1, SEQ ID NO:2, or SEQ ID NO:3; and/or amino acids 1 to 261 of SEQ ID NO:l, SEQ ID NO:2, or SEQ ID NO:3.
  • the polypeptides of the invention comprise the de-immunized Shiga toxin effector region derived from amino acids 1 to 241 SEQ ID NO:l, SEQ ID NO:2, or SEQ ID NO:3. [25]
  • the polypeptides of the invention comprise the de-immunized Shiga toxin effector region comprising or consisting essentially of any one of SEQ ID NOs: 4-52.
  • Certain embodiments of the invention provide a protein comprising a binding region for cell targeting linked to a de-immunized Shiga-toxin-Subunit- A derived region which exhibits one or more Shiga toxin effector function(s), e.g. cytotoxic activity.
  • the proteins of the invention comprise a de-immunized Shiga toxin effector region comprising a polypeptide of the invention and a binding region comprising one or more polypeptides which are capable of specifically binding at least one extracellular target biomolecule.
  • the binding region comprises a polypeptide selected from the group consisting of: a complementary determining region 3 (CDR3) fragment constrained FR3-CDR3- FR4 (FR3-CDR3-FR4) polypeptide, single-domain antibody fragment (sdAb), nanobody, heavy-chain antibody domain derived from a camelid (VHH)
  • CDR3 complementary determining region 3
  • sdAb single-domain antibody fragment
  • VHH heavy-chain antibody domain derived from a camelid
  • scFv single-chain variable fragment
  • Fv antibody variable fragment
  • Fab antigen-binding fragment
  • SIP small modular immunopharmaceutical domain
  • fibronection-derived 10 th fibronectin type III domain (10Fn3) e.g. monobody
  • tenacsin type III domain e.g.
  • TNfn3 ankyrin repeat motif domain
  • ARD ankyrin repeat motif domain
  • a domain of LDLR or LDLR-A low-density-lipoprotein-receptor-derived A-domain
  • lipocalin anti-calin
  • Kunitz domain Protein-A-derived Z domain
  • gamma-B crystalline-derived domain Affilin
  • ubiquitin-derived domain Sac7d-derived polypeptide
  • Fyn-derived SH2 domain affitin
  • miniprotein C- type lectin-like domain scaffold
  • engineered antibody mimic any genetically manipulated counterparts of any of the foregoing that retain binding
  • the cytotoxic protein upon administration of the de-immunized cytotoxic protein of the present invention to a cell physically coupled with an extracellular target biomolecule of the binding region of the cytotoxic protein, the cytotoxic protein is capable of causing death of the cell.
  • the cytotoxic protein upon administration of the de-immunized cytotoxic protein of the present invention to two different populations of cell types with respect to the presence of an extracellular target biomolecule, is capable of causing cell death to the cell- types physically coupled with an extracellular target biomolecule of its binding region at a CD50 at least three times or less than the CD50 to cell types which are not physically coupled with an extracellular target biomolecule of the cytotoxic protein's binding region.
  • the binding region is designed or selected by its ability to bind an extracellular target biomolecule selected from the group consisting of: CD20, CD22, CD40, CD79, CD25, CD30, HER2/neu/ErbB2, EGFR, EpCAM, EphB2, prostate-specific membrane antigen, Cripto, CDCP 1, endoglin, fibroblast activated protein, Lewis-Y, CD19, CD21, CS1/ SLAMF7, CD33, CD52, EpCAM, CEA, gpA33, Mucins, TAG-72, carbonic anhydrase IX, folate binding protein, ganglioside GD2, ganglioside GD3, ganglioside GM2, ganglioside Lewis-Y2, VEGFR, Alpha Vbeta3, Alpha5betal, ErbBl/EGFR, Erb3, c-MET, IGF1R, EphA3,
  • TRAIL-Rl TRAIL-R2, RANKL, FAP, Tenascin, CD64, mesothelin, BRCA1, MART- 1/MelanA, gplOO, tyrosinase, TRP-1, TRP-2, MAGE-1, MAGE-3, GAGE- 1/2, BAGE, RAGE, NY-ESO-1, CDK-4, beta-catenin, MUM-1, caspase- 8, KIAA0205, HPVE6, SART-1, PRAME, carcinoembryonic antigen, prostate specific antigen, prostate stem cell antigen, human aspartyl (asparaginyl) beta- hydroxylase, EphA2, HER3/ErbB-3, MUC1, MART- 1/MelanA, gplOO, tyrosinase associated antigen, HPV-E7, Epstein-Barr Virus antigens, Bcr-Abl, alpha-fetoprotein antigen, 17-A1, bladder tumor
  • the proteins of the invention comprise a carboxy -terminal endoplasmic reticulum retention/retrieval signal motif of a member of the KDEL family.
  • the proteins of the present invention comprise a carboxy-terminal endoplasmic reticulum retention/retrieval signal motif is selected from the group consisting of: KDEL, HDEF, HDEL, RDEF, RDEL, WDEL, YDEL, HEEF, HEEL, KEEL, REEL, KAEL, KCEL, KFEL, KGEL, KHEL, KLEL, KNEL, KQEL, KREL, KSEL, KVEL, KWEL, KYEL, KEDL, KIEL, DKEL, FDEL, KDEF, KKEL, HADL, HAEL, HIEL, HNEL, HTEL, KTEL, HVEL, NDEL, QDEL, REDL, RNEL, RTDL,
  • the protein of the present invention comprises a binding region and a de-immunized Shiga toxin effector region which are physically oriented within the protein such that said binding region is not located adjacent to the amino-terminus of the Shiga toxin effector region.
  • the proteins of the present invention comprise a Shiga toxin effector region derived from amino acids 75 to 251 of SEQ ID NO: l, SEQ ID NO:2, or SEQ ID NO:3.
  • Certain further embodiments provide proteins in which the Shiga toxin effector region is derived from amino acids 1 to 251 of SEQ ID NO: l, SEQ ID NO:2, or SEQ ID NO:3; and/or amino acids 1 to 261 of SEQ ID NO: 1, SEQ ID NO:2, or SEQ ID NO:3.
  • the proteins of the present invention comprise a Shiga toxin effector region is derived from amino acids 1 to 241 SEQ ID NO: l, SEQ ID NO:2, or SEQ ID NO:3.
  • the proteins of the invention comprise the de- immunized Shiga toxin effector region comprising or consisting essentially of any one of SEQ ID NOs: 4-52.
  • the protein of the present invention comprises or consists essentially of SEQ ID NO:53, SEQ ID NO:54, SEQ ID NO:55, SEQ ID NO:56, SEQ ID NO:57, SEQ ID NO:58, or SEQ ID NO:59.
  • the proteins of the invention comprise a de- immunized Shiga toxin effector region which further comprises a mutation relative to a naturally occurring A Subunit of a member of the Shiga toxin family that changes the enzymatic activity of the Shiga toxin effector region, the mutation selected from at least one amino acid residue deletion or substitution, such as, e.g., A231E, R75A, Y77S, Y114S, E167D, R170A, R176K and/or W203A in SEQ ID NO: 1, SEQ ID NO:2, or SEQ ID NO:3.
  • the proteins of the present invention comprise a mutation which reduces or eliminates catalytic activity but retains at least one other Shiga toxin effector function(s).
  • the present invention also provides pharmaceutical compositions comprising a polypeptide and/or protein of the invention and at least one pharmaceutically acceptable excipient or carrier; and the use of such a protein or a composition comprising it in methods of the invention as further described herein.
  • polynucleotides capable of encoding a polypeptide comprising a de- immunized Shiga toxin effector region or protein of the present invention comprising a de-immunized Shiga toxin effector region of the invention are within the scope of the present invention, as well as expression vectors which comprise a polynucleotide of the invention and host cells comprising an expression vector of the invention.
  • Host cells comprising an expression vector may be used, e.g., in methods for producing a polypeptide and/or protein of the invention, or a polypeptide component or fragment thereof, by recombinant expression.
  • the present invention provides methods of selectively killing cell(s) comprising the step of contacting a cell(s) with a protein of the invention or a pharmaceutical composition comprising such a protein of the invention.
  • the step of contacting the cell(s) occurs in vitro. In certain other embodiments, the step of contacting the cell(s) occurs in vivo.
  • the present invention further provides methods of treating diseases, disorders, and/or conditions in patients in need thereof comprising the step of administering to a patient in need thereof a therapeutically effective amount of a composition comprising a de-immunized Shiga toxin effector region polypeptide of the invention, a polypeptide and/or protein comprising it, or a composition comprising any of the foregoing (e.g., a pharmaceutical composition).
  • a composition comprising a de-immunized Shiga toxin effector region polypeptide of the invention, a polypeptide and/or protein comprising it, or a composition comprising any of the foregoing (e.g., a pharmaceutical composition).
  • the disease, disorder, or condition to be treated using this method of the invention is selected from: a cancer, tumor, immune disorder, or microbial infection.
  • the cancer to be treated is selected from the group consisting of: bone cancer, breast cancer, central/peripheral nervous system cancer, gastrointestinal cancer, germ cell cancer, glandular cancer, head-neck cancer, hematological cancer, kidney- urinary tract cancer, liver cancer, lung/pleura cancer, prostate cancer, sarcoma, skin cancer, and uterine cancer.
  • the immune disorder to be treated is an immune disorder associated with a disease selected from the group consisting of: amyloidosis, ankylosing spondylitis, asthma, Crohn's disease, diabetes, graft rejection, graft-versus-host disease, Hashimoto's thyroiditis, hemolytic uremic syndrome, HIV-related diseases, lupus erythematosus, multiple sclerosis, polyarteritis, psoriasis, psoriatic arthritis, rheumatoid arthritis, scleroderma, septic shock, Sjorgren's syndrome, ulcerative colitis, and vasculitis.
  • a disease selected from the group consisting of: amyloidosis, ankylosing spondylitis, asthma, Crohn's disease, diabetes, graft rejection, graft-versus-host disease, Hashimoto's thyroiditis, hemolytic uremic syndrome, HIV-related diseases, lupus erythematosus, multiple sclerosis
  • compositions comprising a de-immunized Shiga toxin effector region polypeptide of the invention, a polypeptide and/or protein comprising it, or a composition comprising any of the foregoing, for the treatment or prevention of a cancer, tumor, immune disorder, or microbial infection.
  • a composition of matter of the invention in the manufacture of a medicament for the treatment or prevention of a cancer, tumor, immune disorder, or microbial infection.
  • the proteins of the present invention may be used to deliver one or more additional exogenous materials into a cell physically coupled with an extracellular target biomolecule of the protein of the present invention.
  • the present invention provides a method for delivering exogenous material to the inside of a cell(s) comprising contacting the cell(s), either in vitro or in vivo, with a protein, pharmaceutical composition, and/or diagnostic composition of the present invention.
  • the present invention further provides a method for delivering exogenous material to the inside of a cell(s) in a patient in need thereof, the method comprising the step of administering to the patient a protein of the present invention, wherein the target cell(s) is physically coupled with an extracellular target biomolecule of the protein of the present invention.
  • composition e.g. a pharmaceutical composition or diagnostic composition
  • a diagnostic composition comprising a de-immunized Shiga toxin effector region polypeptide of the invention, a polypeptide and/or protein comprising it, or a composition comprising any of the foregoing, and a detection promoting agent for the collection of information, such as diagnostically useful information about a cell type, tissue, organ, disease, disorder, condition, or patient.
  • the method of detecting a cell using a protein and/or diagnostic composition of the invention comprising the steps of contacting a cell with said protein and/or diagnostic composition and detecting the presence of said protein and/or diagnostic composition.
  • the step of contacting the cell(s) occurs in vitro.
  • the step of contacting the cell(s) occurs in vivo.
  • the step of detecting the cell(s) occurs in vitro.
  • the step of detecting the cell(s) occurs in vivo.
  • a diagnostic composition of the invention may be used to detect a cell in vivo by administering to a mammalian subject a composition comprising protein of the present invention which comprises a detection promoting agent and then detecting the presence of the protein of the present invention either in vitro or in vivo.
  • the information collected may regard the presence of a cell physically coupled with an extracellular target of the binding region of the protein of the present invention and may be useful in the diagnosis, prognosis, characterization, and/or treatment of a disease, disorder, or condition.
  • Certain compounds (e.g. polypeptides and proteins) of the invention, compositions (e.g. pharmaceutical compositions and diagnostic compositions) of the invention, and methods of the invention may be used to determine if a patient belongs to a group that responds to a pharmaceutical composition of the invention.
  • kits comprising a composition of matter of the present invention, and optionally, instructions for use, additional reagent(s), and/or pharmaceutical delivery device(s).
  • Figure 1 shows the general arrangement of exemplary de-immunized polypeptides and cytotoxic proteins.
  • Figure 2 shows that the D58A substitution in a de-immunized Shiga toxin effector region effectively disrupted the epitope recognized by pAb2 under denaturing conditions and reduced the antigenicity of the polypeptide comprising a Shiga toxin effector region.
  • Figure 3 shows that the D58A substitution in the context of multiple epitope region disruption variants of de-immunized Shiga toxin effector regions effectively disrupted the epitope recognized by pAb2 under denaturing conditions and reduced the antigenicity of the polypeptide a Shiga toxin effector region.
  • Figure 4 shows that multiple-epitope-region-disruption variants of de- immunized Shiga toxin effector regions disrupted the epitopes recognized by pAb2 and mAbl under denaturing conditions. These multiple-epitope-region- disruption variants have reduced antigenicity as compared to a polypeptide comprising the parental, wild-type, Shiga toxin effector region.
  • Figure 5 shows that multiple-epitope-region-disruption variants of de- immunized Shiga toxin effector regions effectively disrupted the epitopes recognized by pAb2 and/or mAbl under denaturing conditions. These multiple- epitope-region-disruption variants have reduced antigenicity as compared to a polypeptide comprising the parental, wild-type, Shiga toxin effector region.
  • Figure 6 shows that a de-immunized Shiga toxin effector region comprising multiple epitope-region disruptions resulted in a very effective disruption of the epitope recognized by mAbl under native protein folding conditions.
  • This multiple-epitope-region-disruption variant had reduced antigenicity as compared to a polypeptide comprising the parental, wild-type, Shiga toxin effector region.
  • Figure 7 shows that a de-immunized Shiga toxin effector region comprising multiple epitope-region disruptions resulted in reduced, in vivo, antibody response(s) by a mammalian immune system.
  • This multiple-epitope- region-disruption variant had reduced immunogenicity as compared to a polypeptide comprising the parental, wild-type, Shiga toxin effector region.
  • the term "and/or" when referring to two species, A and B means at least one of A and B.
  • the term “and/or” when referring to greater than two species, such as A, B, and C means at least one of A, B, or C, or at least one of any combination of A, B, or C (with each species in singular or multiple possibility).
  • amino acid residue or “amino acid” includes reference to an amino acid that is incorporated into a protein, polypeptide, or peptide.
  • polypeptide includes any polymer of amino acids or amino acid residues.
  • polypeptide sequence refers to a series of amino acids or amino acid residues which physically comprise a polypeptide.
  • a "protein” is a
  • amino acid sequence refers to a series of amino acids or amino acid residues which physically comprise a peptide or polypeptide depending on the length. Unless otherwise indicated, polypeptide and protein sequences disclosed herein are written from left to right representing their order from an amino terminus to a carboxy terminus.
  • amino acid includes naturally occurring amino acids and, unless otherwise limited, also include known analogs of natural amino acids that can function in a similar manner as naturally occurring amino acids, such as selenocysteine, pyrrolysine, N-formylmethionine, gamma-carboxyglutamate, hydroxyprolinehypusine, pyroglutamic acid, and selenomethionine.
  • amino acids referred to herein are described by shorthand designations as follows in Table A:
  • the terms “expressed,” “expressing,” or “expresses” and grammatical variants thereof refer to translation of a polynucleotide or nucleic acid into a polypeptide or protein.
  • the expressed polypeptide or proteins may remain intracellular, become a component of the cell surface membrane or be secreted into an extracellular space.
  • immunoglobulin-type binding region based on its capability of binding to the biomolecule following the symbol.
  • the symbol means the polypeptide regions before and after it are physically linked together to form a continuous polypeptide.
  • the phrase "derived from” means the polypeptide region comprises amino acid sequences originally found in a protein and may now comprise additions, deletions, truncations, or other alterations from the original sequence such that overall function and structure are substantially conserved.
  • effector means providing a biological activity, such as cytotoxicity, biological signaling, enzymatic catalysis, subcellular routing, and/or intermolecular binding resulting in the recruit of a factor(s) and/or an allosteric effect(s).
  • a Shiga toxin effector function is a biological activity conferred by a polypeptide region derived from a Shiga toxin A Subunit.
  • Shiga toxin effector functions include cellular internalization, subcellular routing, catalytic activity, and cytotoxicity.
  • Non-limiting examples of Shiga toxin catalytic activities include ribosome inactivation, protein synthesis inhibition, N-glycosidase activity,
  • polynucleotide adenosine glycosidase activity, RNAase activity, and DNAase activity.
  • RIPs can depurinate nucleic acids, polynucleosides, polynucleotides, rRNA, ssDNA, dsDNA, mRNA (and poly A), and viral nucleic acids
  • Shiga toxin catalytic activities have been observed both in vitro and in vivo.
  • Assays for Shiga toxin effector activity can measure various activities, such as, e.g., protein synthesis inhibitory activity, depurination activity, inhibition of cell growth, cytotoxicity, supercoiled DNA relaxation activity, and/or nuclease activity.
  • cytotoxic activity of a cytotoxic protein refers to the relative levels of cytotoxicity between a targeted cell population and a non-targeted bystander cell population, which can be expressed as a ratio of the half- maximal cytotoxic concentration (CD50) for a targeted cell type over the CD50 for an untargeted cell type to show
  • the retention of Shiga toxin effector function refers to a level of Shiga toxin functional activity, as measured by an appropriate quantitative assay with reproducibility, comparable to a wild-type Shiga toxin effector polypeptide control.
  • retained Shiga toxin effector function is exhibiting an ICso of 10,000 pM or less.
  • retained Shiga toxin effector function is exhibiting a CD50 of 1,000 nM or less, depending on the cell type and its expression of the appropriate extracellular target biomolecule.
  • de-immunized means reduced antigenic and/or immunogenic potential after administration to a mammal. This includes a reduced antigenic and/or immunogenic potential overall despite the introduction of one or more new epitopes.
  • the present invention provides improved polypeptides derived from A Subunits of members of the Shiga toxin family with reduced immunogenic potential. These improved Shiga toxin effector polypeptides may be utilized in various compositions, e.g. cytotoxic therapeutics, therapeutic delivery agents, diagnostic molecules, and immunization materials.
  • Shiga toxins tend to be immunogenic to mammals. Unwanted immunogenicity in protein therapeutics has resulted in reduced efficacy, unpredictable pharmacokinetics, and undesirable immune responses that limit dosages and repeat administrations. Although there is a need for molecules comprising de-immunized Shiga-toxin-derived polypeptides that have reduced immunogenic potential to help avoid unwanted immune responses, there exists no predictable method to successfully identify and remove internal B-cell epitopes while maintaining Shiga toxin effector function(s).
  • the main challenge is silencing epitopes within the Shiga toxin polypeptide's effector domains, e.g. its enzymatic domain, while retaining the desired Shiga toxin effector functions, e.g., potent ribosome inhibition and directing subcellular routing. While these internal epitopes may be diminished or abolished by mutation and/or chemical modification, the challenge is to do so while preserving Shiga toxin effector functions.
  • Shiga toxin effector functions The antigenicity and/or immunogenicity of each epitope is predicted to be reduced or eliminated by the amino acid substitutions provided, which in turn reduces the overall antigenicity and/or immunogenicity of any compositions of matter comprising at least one provided epitope disruption.
  • the de-immunized Shiga toxin effector polypeptides which were identified as having reduced immunogenic potential while maintaining Shiga toxin function(s), were not predictable a priori, despite attempts at de- immunization of distantly related bacterial protein toxins, such as Pseudomonas exotoxin A.
  • Polypeptides comprising de-immunized Shiga toxin effector regions of the invention may be used as components of recombinant immunotoxins and ligand-toxin fusions for the targeted killing of specific cell types and the treatment of a variety of diseases, including cancers, immune disorders, and microbial infections. Additionally, the polypeptides of the invention may be used as components of cell-type specific internalizing molecules for the precise delivery of exogenous materials, such as detection promoting agents for diagnostic information gathering. Further, the polypeptides of the invention, independently or as components of Shiga holotoxins, may be used in
  • the present invention provides various polypeptides comprising Shiga toxin effector regions with reduced immunogenic potential but which retain Shiga toxin effector functionality(s), such as cellular internalization, subcellular routing, catalytic activity, and cytotoxicity.
  • a polypeptide of the invention comprises a Shiga toxin effector region comprising a disruption of at least one epitope region described herein.
  • a protein of the invention comprises a de- immunized Shiga toxin effector region and a binding region comprising one or more polypeptides capable of specifically binding at least one extracellular target biomolecule.
  • the Shiga toxin family of protein toxins is composed of various naturally occurring toxins that are structurally and functionally related, e.g., Shiga toxin, Shiga-like toxin 1 , and Shiga-like toxin 2 (Johannes L, R5mer W, Nat Rev Microbiol 8: 105-16 (2010)). Members of the Shiga toxin family share the same overall structure and mechanism of action (Engedal, N et al, Microbial Biotech 4: 32-46 (201 1)).
  • Stx, SLT-1 and SLT-2 display indistinguishable enzymatic activity in cell free systems (Head S et al, J Biol Chem 266: 3617-21 (1991); Tesh V et al, Infect Immun 61 : 3392-402 (1993); Brigotti M et al, Toxicon 35: 1431-1437 (1997)).
  • the phrase "Shiga toxin effector region” refers to a polypeptide region derived from a Shiga toxin A Subunit of a member of the Shiga toxin family that is capable of exhibiting at least one Shiga toxin function.
  • Shiga toxin functions include, e.g., cell entry, lipid membrane deformation, directing subcellular routing, avoiding degradation, catalytically inactivating ribosomes, effectuating cytotoxicity, and effectuating cytostatic effects.
  • the retention of "significant" Shiga toxin effector function refers to a level of Shiga toxin functional activity, as measured by an appropriate quantitative assay with reproducibility comparable to a wild-type Shiga toxin effector polypeptide control.
  • significant Shiga toxin effector function is exhibiting an ICso of 300 pM or less depending on the source of the ribosomes (e.g. bacteria, archaea, or eukaryote (algae, fungi, plants, or animals)).
  • the failure to detect activity in Shiga toxin effector function may be due to improper expression, polypeptide folding, and/or polypeptide stability rather than a lack of cell entry, subcellular routing, and/or enzymatic activity.
  • Assays for Shiga toxin effector functions may not require much polypeptide of the invention to measure significant amounts of Shiga toxin effector function activity.
  • an underlying cause of low or no effector function is determined empirically to relate to protein expression or stability, one of skill in the art may be able to compensate for such factors using protein chemistry and molecular engineering techniques known in the art, such that a Shiga toxin functional effector activity may be restored and measured.
  • improper cell based expression may be compensated for by using different expression control sequences; improper polypeptide folding and/or stability may benefit from stabilizing terminal sequences, or compensatory mutations in non- effector regions which stabilize the three dimensional structure of the protein, etc.
  • de-immunized Shiga toxin effector polypeptides may be analyzed for any level of those Shiga toxin effector functions, such as a being within 1000-fold or 100- fold or less the activity of a wild-type Shiga toxin effector polypeptide or exhibiting 3 -fold to 30-fold or greater activity as compared to a functional knockout Shiga toxin effector polypeptide.
  • Shiga toxin effector functions are not easily measurable, e.g. subcellular routing functions.
  • Shiga toxin effector polypeptides with even considerably reduced Shiga toxin effector functions, such as, e.g., subcellular routing or cytotoxicity, as compared to wild-type Shiga toxin effector polypeptides may still be potent enough for practical applications involving targeted cell killing and/or specific cell detection.
  • the Shiga toxin family encompasses true Shiga toxin (Stx) isolated from S. dysenteriae serotype 1, Shiga-like toxin 1 variants (SLT1 or Stxl or SLT-1 or Slt-I) isolated from serotypes of enterohemorrhagic E. coli, and Shiga-like toxin 2 variants (SLT2 or Stx2 or SLT-2) isolated from serotypes of
  • SLT1 enterohemorrhagic E. coli.
  • SLT1 differs by only one residue from Stx, and both have been referred to as Verocytotoxins or Verotoxins (VTs) (O'Brien, Curr Top Microbiol Immunol 180: 65-94 (1992)).
  • VTs Verocytotoxins
  • SLT1 and SLT2 variants are only about 53-60% similar to each other at the amino acid sequence level, they share mechanisms of enzymatic activity and cytotoxicity common to the members of the Shiga toxin family (Johannes, Nat Rev Microbiol 8: 105-16 (2010)).
  • Shiga toxins Over 39 different Shiga toxins have been described, such as the defined subtypes Stxla, Stxlc, Stxld, and Stx2a-g (Scheutz F et al, J Clin Microbiol 50: 2951-63 (2012)).
  • Members of the Shiga toxin family are not naturally restricted to any bacterial species because Shiga-toxin-encoding genes can spread among bacterial species via horizontal gene transfer (Strauch E et al., Infect Immun 69: 7588-95 (2001); Zhaxybayeva O, Doolittle W, Curr Biol 21 : R242-6 (2011)).
  • interspecies transfer As an example of interspecies transfer, a Shiga toxin was discovered in a strain of A.
  • Shiga toxin amino acid sequence is presumed to be capable of developing slight sequence variations due to genetic drift and/or selective pressure while still maintaining a mechanism of cytotoxicity common to members of the Shiga toxin family (see Scheutz, J Clin Microbiol 50: 2951-63 (2012)).
  • the polypeptides of the invention comprise Shiga toxin effector regions derived from an A Subunit of a member of the Shiga toxin family with at least one putative epitope region disrupted in order to reduce the antigenic and/or immunogenic potential of the polypeptides after administration to a mammal.
  • the term "disrupted” or “disruption” as used herein with regard to an epitope region refers to the deletion of at least one amino acid in an epitope region, inversion of two or more amino acids where at least one of the inverted amino acids is in an epitope region, insertion of at least one amino acid in an epitope region, and mutation of at least one amino acid in an epitope region.
  • An epitope region disruption by mutation includes amino acid substitutions with nonstandard amino acids and/or non-natural amino acids.
  • Epitope regions may alternatively be disrupted by mutations comprising the modification of an amino acid by the addition of a covalently-linked chemical structure which masks at least one amino acid in an epitope region, see, e.g. PEGylation (see Zhang C et al, BioDrugs 26: 209-15 (2012) and small molecule adjuvants (Flower D, Expert Opin Drug Discov 7: 807-17 (2012)).
  • Certain epitope regions and disruptions are indicated herein by reference to specific amino acid positions of native Shiga toxin A Subunits provided in the Sequence Listing, noting that naturally occurring Shiga toxin A Subunits may comprise precursor forms containing signal sequences of about 22 amino acids at their amino-terminals which are removed to produce mature Shiga toxin A Subunits and are recognizable to the skilled worker. Further, certain epitope region disruptions are indicated herein by reference to specific amino acids (e.g. S for a serine residue) natively present at specific positions within native Shiga toxin A Subunits (e.g.
  • S33 for the serine residue at position 33 from the amino terminus followed by the amino acid with which that residue has been substituted in the particular mutation under discussion (e.g. S33I represents the amino acid substitution of isoleucine for serine at amino acid residue 33 from the amino terminus).
  • Certain embodiments of the invention provide polypeptides comprising a Shiga toxin effector region comprising an amino acid sequence derived from an A Subunit of a member of the Shiga toxin Family, the Shiga toxin effector region comprising a disruption of at least one epitope region provided herein (see e.g. Tables 1, 2, and 3).
  • a de- immunized Shiga toxin effector region polypeptide of the invention may comprise or consist essentially of full-length Shiga toxin A Subunit (e.g.
  • SLT-1A (SEQ ID NO: l), StxA (SEQ ID NO:2), or SLT-2A (SEQ ID NO:3)) comprising at least one disruption of the amino acid sequence selected from the group of natively positioned amino acids consisting of: 1-15 of SEQ ID NO: 1 or SEQ ID NO:2; 3-14 of SEQ ID O:3; 26-37 of SEQ ID NO:3; 27-37 of SEQ ID NO: l or SEQ ID NO:2; 39-48 of SEQ ID NO: l or SEQ ID NO:2; 42-48 of SEQ ID NO:3; 53- 66 of SEQ ID O: l, SEQ ID O:2, or SEQ ID O:3; 94-1 15 of SEQ ID O: l, SEQ ID O:2, or SEQ ID O:3; 141-153 of SEQ ID NO: 1 or SEQ ID NO:2; 140-156 of SEQ ID NO:3; 179-190 of SEQ ID NO: l or SEQ ID NO:2;
  • a Shiga toxin effector region polypeptide of the invention may comprise or consist essentially of a truncated Shiga toxin A Subunit. Truncations of Shiga toxin A Subunits might result in the deletion of entire epitope regions without affecting toxin effector catalytic activity and cytotoxicity. The smallest Shiga toxin A Subunit fragment exhibiting significant enzymatic activity is a polypeptide composed of residues 75-247 of StxA (Al- Jaufy, Infect Immun 62: 956-60 (1994)).
  • Truncating the carboxy-terminus of SLT-1A, StxA, or SLT-2A to amino acids 1-251 removes two predicted B-cell epitope regions, two predicted CD4 positive (CD4+) T-cell epitopes, and a predicted discontinuous B-cell epitope.
  • Truncating the amino-terminus of SLT- 1A, StxA, or SLT-2A to 75-293 removes at least three predicted B-cell epitope regions and three predicted CD4+ T-cell epitopes.
  • Truncating both amino- and carboxy -terminals of SLT-1A, StxA, or SLT-2A to 75-251 deletes at least five predicted B-cell epitope regions, four putative CD4+ T-cell epitopes, and one predicted discontinuous B-cell epitope.
  • a Shiga toxin effector region polypeptide of the invention may comprise or consist essentially of a full-length or truncated Shiga toxin A Subunit with at least one mutation, e.g. deletion, insertion, inversion, or substitution, in a provided epitope region.
  • the polypeptides comprise a disruption which comprises a deletion of at least one amino acid within the epitope region.
  • the polypeptides comprise a disruption which comprises an insertion of at least one amino acid within the epitope region.
  • the polypeptides comprise a disruption which comprises an inversion of amino acids, wherein at least one inverted amino acid is within the epitope region.
  • the polypeptides comprise a disruption which comprises a mutation, such as an amino acid substitution to a non-standard amino acid or an amino acid with a chemically modified side chain. Numerous examples of single amino acid substitutions are provided in the Examples.
  • the Shiga toxin effector region polypeptides of the invention may comprise or consist essentially of a full-length or truncated Shiga toxin A Subunit with one or more mutations as compared to the native sequence which comprises at least one amino acid substitution selected from the group consisting of: A, G, V, L, I, P, C, M, F, S, D, N, Q, H, and K.
  • the polypeptide may comprise or consist essentially of a full-length or truncated Shiga toxin A Subunit with a single mutation as compared to the native sequence wherein the substitution is selected from the group consisting of: D to A, D to G, D to V, D to L, D to I, D to F, D to S, D to Q, E to A, E to G, E to V, E to L, E to I, E to F, E to S, E to Q, E to N, E to D, E to M, E to R, G to A, H to A, H to G, H to V, H to L, H to I, H to F, H to M, K to A, K to G, K to V, K to L, K to I, K to M, K to H, L to A, L to G, N to A, N to G, N to V, N to L, N to I, N to F, P to A, P to G, P to F, R to A, R to G, R, R, R to
  • the Shiga toxin effector region polypeptides of the invention comprise or consist essentially of a full-length or truncated Shiga toxin A Subunit with one or more mutations as compared to the native amino acid residue sequence which comprises at least one amino acid substitution within an epitope region, wherein at least one substitution occurs at the natively positioned group of amino acids selected from the group consisting of: 1 of SEQ ID NO: 1 or SEQ ID NO:2; 4 of SEQ ID NO: 1, SEQ ID NO:2, or SEQ ID NO:3; 8 of SEQ ID NO: 1, SEQ ID NO:2, or SEQ ID NO:3; 9 of SEQ ID NO: 1, SEQ ID NO:2, or SEQ ID NO:3; 11 of SEQ ID NO: 1, SEQ ID NO:2, or SEQ ID NO:3; 33 of SEQ ID NO: 1 or SEQ ID NO:2; 43 of SEQ ID NO: 1 or SEQ ID NO:2; 45 of SEQ ID NO: 1 or SEQ ID NO:
  • the Shiga toxin effector region polypeptides of the invention comprise or consist essentially of a full-length or truncated Shiga toxin A Subunit with at least one substitution within an epitope region, wherein at least one amino acid substitution is to a non-conservative amino acid (see, e.g., Table B, infra) relative to a natively occurring amino acid positioned at one of the following native positions: 1 of SEQ ID NO: 1 or SEQ ID NO:2; 4 of SEQ ID NO:l, SEQ ID NO:2, or SEQ ID NO:3; 8 of SEQ ID NO: 1, SEQ ID NO:2, or SEQ ID NO:3; 9 of SEQ ID NO: 1, SEQ ID NO:2, or SEQIDNO:3; 11 of SEQ ID NO:l, SEQ ID NO:2, or SEQ ID NO:3; 33 of SEQ ID NO: 1 or SEQ ID NO:2; 43 of SEQ ID NO: 1 or SEQ ID NO:
  • the Shiga toxin effector region polypeptides of the invention comprise or consist essentially of a full-length or truncated Shiga toxin A Subunit with at least one amino acid substitution selected from the group consisting of: Kl to A, G, V, L, I, F, M and H; T4 to A, G, V, L, I, F, M, and S; S8 to A, G, V, I, L, F, and M; T9 to A, G, V, I, L, F, M, and S; S9 to A, G, V, L, I, F, and M; Kl 1 to A, G, V, L, I, F, M and H; S33 to A, G, V, L, I, F, and M; S45 to A, G, V, L, I, F, and M; T45 to A, G, V, L, I, F, and M; D47 to A, G, V, L, I, F, S, and Q
  • the Shiga toxin effector region polypeptides of the invention comprise or consist essentially of a full-length or truncated Shiga toxin A Subunit with at least one of the following amino acid substitutions KIM, T4I, S8I, T8V, T9I, S9I, K11A, K11H, S33I, S45I, T45I, D47G, N48V, N48F, L49A, D53A, D53G, D53N, R55A, R55V, R55L, D58A, D58F, P59A, P59F, E60I, E60T, E60R, E61A, E61V, E61L, G62A, D94A, S96I, S109V, T109V, G110A, SI 12V, G147A, R179A, T180G, T181I, D183A, D183G, D184A, D184F, L185V, S186A,
  • epitope disrupting substitutions may be combined to form a de-immunized Shiga toxin effector polypeptide with multiple substitutions per epitope region and/or multiple epitope regions disrupted while still retaining Shiga toxin effector function.
  • substitutions at the natively positioned residues Kl, T4, S8, T8, T9, S9, Kl 1, Kl 1, S33, S45, T45, D47, N48, L49, D53, R55, D58, P59, E60, E61, G62, D94, S96I, S109, T109, G110, SI 12, G147, R179, T180, T181I, D183, D184, L185, S 186, S186, G187, R188, S 189, R204A, R205, S247, Y247, R248, R250, R251, D264, G264, T286 and/or T286 may be combined, where possible, with substitutions at the natively positioned residues Kl, T4, S8, T8, T9, S9, Kl 1, Kl 1, S33, S45, T45, D47, N48, L49, D53, R55, D58, P59, E60, E61, G62, D94, S96I
  • the Shiga toxin effector region polypeptides of the invention comprises or consists essentially of a truncated Shiga toxin A Subunit which is shorter than a full-length Shiga toxin A Subunit wherein at least one amino acid is disrupted in a natively positioned epitope region provided in the Examples (Tables 1, 2, 3, 4, and/or 5).
  • Shiga-like toxin 1 A Subunit truncations are catalytically active, capable of enzymatically inactivating ribosomes in vitro, and cytotoxic when expressed within a cell (LaPointe, J Biol Chem 280: 23310- 18 (2005)).
  • the smallest Shiga toxin A Subunit fragment exhibiting full enzymatic activity is a polypeptide composed of residues 1-239 of SltlA (LaPointe, J Biol Chem 280: 23310-18 (2005)). Although the smallest fragment of the Shiga toxin A Subunit reported to retain substantial catalytic activity was residues 75-247 of StxA (Al-Jaufy, Infect Immun 62: 956-60 (1994)), a StxA truncation expressed de novo within a eukaryotic cell requires only up to residue 240 to reach the cytosol and exert catalytic inactivation of ribosomes (LaPointe, J Biol Chem 280: 23310-18 (2005)).
  • de-immunized Shiga toxin effector region polypeptides of the invention may commonly be smaller than the full length A subunit, it is preferred that the de-immunized Shiga toxin effector region maintain the polypeptide region from amino acid position 77 to 239 (SLT-IA (SEQ ID NO: l) or StxA (SEQ ID NO:2)) or the equivalent in other A Subunits of members of the Shiga toxin family (e.g. 77 to 238 of (SEQ ID NO:3)).
  • the Shiga toxin effector region polypeptides derived from SLT-IA may comprise or consist essentially of amino acids 75 to 251 of SEQ ID NO: 1, 1 to 241 of SEQ ID NO: 1, 1 to 251 of SEQ ID NO: 1, or amino acids 1 to 261 of SEQ ID NO: 1 wherein at least one amino acid is disrupted in the natively positioned epitope regions provided in the Examples (Tables 1, 2, 3, 4, and/or 5).
  • de-immunized Shiga toxin effector regions derived from StxA may comprise or consist essentially of amino acids 75 to 251 of SEQ ID NO:2, 1 to 241 of SEQ ID NO:2, 1 to 251 of SEQ ID
  • Shiga toxin effector regions derived from SLT-2 may comprise or consist essentially of amino acids 75 to 251 of SEQ ID NO:3, 1 to 241 of SEQ ID NO:3, 1 to 251 of SEQ ID
  • the invention further provides variants of the polypeptides of the invention, wherein the Shiga toxin effector region differs from a naturally occurring Shiga toxin A Subunit by only or up to 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20, 25, 30, 35, 40 or more amino acid residues (but by no more than that which retains at least 85%, 90%, 95%, 99% or more amino acid sequence identity).
  • a Shiga toxin effector region polypeptide of the invention derived from an A Subunit of a member of the Shiga toxin family may comprise additions, deletions, truncations, or other alterations from the original sequence so long as at least 85%, 90%, 95%, 99% or more amino acid sequence identity is maintained to a naturally occurring Shiga toxin A Subunit and at least one amino acid is disrupted in at least one natively positioned epitope region provided in the Examples (Tables 1, 2, 3, 4, and/or 5).
  • the Shiga toxin effector region polypeptides comprises or consists essentially of amino acid sequences having at least 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, 97%, 98%, 99%, 99.5% or 99.7% overall sequence identity to a naturally occurring Shiga toxin A Subunit, such as SLT-IA (SEQ ID N0: 1), StxA (SEQ ID N0:2), and/or SLT-2A (SEQ ID NO:3) wherein at least one amino acid is disrupted in at least one natively positioned epitope region provided in the Examples (Tables 1, 2, 3, 4, and/or 5).
  • SLT-IA SEQ ID N0: 1
  • StxA SEQ ID N0:2
  • SLT-2A SEQ ID NO:3
  • either a full length or a truncated version of the Shiga toxin A Subunit may comprise one or more mutations (e.g. substitutions, deletions, insertions or inversions) so long as at least one amino acid is disrupted in at least one natively positioned epitope region provided in the Examples (Tables 1, 2, 3, 4, and/or 5).
  • the de- immunized Shiga toxin effector region polypeptides have sufficient sequence identity to a naturally occurring Shiga toxin A Subunit to retain cytotoxicity after entry into a cell, either by well-known methods of host cell transformation, trans fection, infection or induction, or by internalization mediated by a cell- targeting binding region linked with the Shiga toxin effector region polypeptide.
  • the most critical residues for enzymatic activity and/or cytotoxicity in the Shiga toxin A Subunits have been mapped to the following residue-positions:
  • the de- immunized Shiga toxin effector region polypeptides may preferably but not necessarily maintain one or more conserved amino acids at positions, such as those found at positions 77, 167, 170, and 176 in StxA, SLT- IA, or the equivalent conserved position in other members of the Shiga toxin family which are typically required for cytotoxic activity.
  • the capacity of a cytotoxic protein of the invention to cause cell death, e.g. its cytotoxicity may be measured using any one or more of a number of assays well known in the art.
  • Proteins of the invention comprise a de-immunized Shiga toxin effector region comprising a polypeptide of the invention linked to an extracellular target biomolecule specific binding region.
  • Binding regions of the proteins of the invention comprise one or more polypeptides capable of selectively and specifically binding an extracellular target biomolecule. Binding regions may comprise one or more various polypeptide moieties, such as ligands whether synthetic or naturally occurring ligands and derivatives thereof, immunoglobulin derived domains, synthetically engineered scaffolds as alternatives to immunoglobulin domains, and the like.
  • binding regions known in the art that are useful for targeting polypeptides to specific cell-types via their binding characteristics, such as ligands, monoclonal antibodies, engineered antibody derivatives, and engineered alternatives to antibodies.
  • the binding region of the protein of the invention comprises a naturally occurring ligand or derivative thereof that retains binding functionality to an extracellular target biomolecule, commonly a cell surface receptor.
  • an extracellular target biomolecule commonly a cell surface receptor.
  • various cytokines, growth factors, and hormones known in the art may be used to target the cytotoxic protein to the cell-surface of specific cell types expressing a cognate cytokine receptor, growth factor receptor, or hormone receptor.
  • ligands include (alternative names are indicated in parentheses) B- cell activating factors (BAFFs, APRIL), colony stimulating factors (CSFs), epidermal growth factors (EGFs), fibroblast growth factors (FGFs), vascular endothelial growth factors (VEGFs), insulin-like growth factors (IGFs), interferons, interleukins (such as IL-2, IL-6, and IL-23), nerve growth factors (NGFs), platelet derived growth factors, transforming growth factors (TGFs), and tumor necrosis factors (TNFs).
  • BAFFs B- cell activating factors
  • CSFs colony stimulating factors
  • EGFs epidermal growth factors
  • FGFs fibroblast growth factors
  • VEGFs vascular endothelial growth factors
  • IGFs insulin-like growth factors
  • interferons interleukins (such as IL-2, IL-6, and IL-23)
  • NGFs nerve growth factors
  • TGFs tumor necros
  • the binding region comprises a synthetic ligand capable of binding an extracellular target biomolecule.
  • a synthetic ligand capable of binding an extracellular target biomolecule.
  • One non-limiting example is antagonists to cytotoxic T-lymphocyte antigen 4 (CTLA-4).
  • the binding region may comprise an immunoglobulin-type binding region.
  • immunoglobulin-type binding region refers to a polypeptide region capable of binding one or more target biomolecules, such as an antigen or epitope. Binding regions may be functionally defined by their ability to bind to target molecules. Immunoglobulin-type binding regions are commonly derived from antibody or antibody-like structures; however, alternative scaffolds from other sources are contemplated within the scope of the term.
  • Immunoglobulin (Ig) proteins have a structural domain known as an Ig domain.
  • Ig domains range in length from about 70-110 amino acid residues and possess a characteristic Ig-fold, in which typically 7 to 9 antiparallel beta strands arrange into two beta sheets which form a sandwich-like structure. The Ig fold is stabilized by hydrophobic amino acid interactions on inner surfaces of the sandwich and highly conserved disulfide bonds between cysteine residues in the strands.
  • Ig domains may be variable (IgV or V-set), constant (IgC or C-set) or intermediate (Igl or I-set).
  • Ig domains may be associated with a complementarity determining region (CDR) which is important for the specificity of antibodies binding to their epitopes.
  • CDR complementarity determining region
  • HGNC HGNC provides a list of members of the Ig-like domain containing family.
  • An immunoglobulin-type binding region may be a polypeptide sequence of an antibody or antigen-binding fragment thereof wherein the amino acid sequence has been varied from that of a native antibody or an Ig-like domain of a non-immunoglobulin protein, for example by molecular engineering or selection by library screening. Because of the relevance of recombinant DNA techniques and in vitro library screening in the generation of immunoglobulin-type binding regions, antibodies can be redesigned to obtain desired characteristics, such as smaller size, cell entry, or other therapeutic improvements. The possible variations are many and may range from the changing of just one amino acid to the complete redesign of, for example, a variable region. Typically, changes in the variable region will be made in order to improve the antigen-binding characteristics, improve variable region stability, or reduce the potential for immunogenic responses.
  • the immunoglobulin-type binding region is derived from an immunoglobulin binding region, such as an antibody paratope capable of binding an extracellular target biomolecule.
  • the immunoglobulin-type binding region comprises an engineered polypeptide not derived from any immunoglobulin domain but which functions like an immunoglobulin binding region by providing high-affinity binding to an extracellular target biomolecule.
  • This engineered polypeptide may optionally include polypeptide scaffolds comprising or consisting essentially of complementary determining regions from immunoglobulins as described herein.
  • binding region of the present proteins is selected from the group which includes single-domain antibody domains (sdAbs), nanobodies, heavy-chain antibody domains derived from camelids (VHH fragments), bivalent nanobodies, heavy-chain antibody domains derived from cartilaginous fishes, immunoglobulin new antigen receptors (IgNARs), VNAR fragments, single-chain variable (scFv) fragments,
  • scFv fragments diabodies, triabodies, tetrabodies
  • bispecific tandem scFv fragments disulfide stabilized antibody variable (Fv) fragments, disulfide stabilized antigen-binding (Fab) fragments consisting of the VL, VH, CL and CH 1 domains, divalent F(ab')2 fragments, Fd fragments consisting of the heavy chain and CHI domains, single chain FV-CH3 minibodies, bispecific minibodies, dimeric CH2 domain fragments (CH2D), FC antigen binding domains (Fcabs), isolated complementary determining region 3 (CDR3) fragments, constrained framework region 3, CDR3, framework region 4 (FR3-CDR3-FR4) polypeptides, small modular immunopharmaceutical (SMIP) domains, and any genetically manipulated counterparts of the foregoing that retain its paratope and binding function (see Saerens D et al, Curr. Opin. Pharmacol 8: 600-8 (2008);
  • the binding region includes engineered, alternative scaffolds to immunoglobulin domains that exhibit similar functional characteristics, such as high-affinity and specific binding of target biomolecules, and enables the engineering of improved characteristics, such as greater stability or reduced immunogenicity.
  • the binding region is selected from the group which includes engineered, fibronection-derived, 10 th fibronectin type III (10Fn3) domain (monobodies, AdNectinsTM, or AdNexinsTM); engineered, tenacs in-derived, tenacsin type III domain (CentrynsTM); engineered, ankyrin repeat motif containing polypeptide (DARPinsTM); engineered, low-density- lipoprotein-receptor-derived, A domain (LDLR-A) (AvimersTM); lipocalin (anticalins); engineered, protease inhibitor-derived, Kunitz domain; engineered, Protein-A-derived, Z domain (AffibodiesTM); engineered, gamma-B crystalline- derived scaffold or engineered, ubiquitin-derived scaffold (Affilins); Sac7d- derived polypeptides (Nanoffitins® or affitins); engineered,
  • binding region component has a dissociation constant of 10 "5 to 10 "12 moles per liter, preferably less than 200 nanomolar (nM), towards an extracellular target biomolecule.
  • Extracellular Target Biomolecules 10 "5 to 10 "12 moles per liter, preferably less than 200 nanomolar (nM)
  • the binding region of the protein of the invention comprises a polypeptide region capable of binding specifically to an extracellular target biomolecule, preferably which is physically-coupled to the surface of a cell type of interest, such as a cancer cell, tumor cell, plasma cell, infected cell, or host cell harboring an intracellular pathogen.
  • a cell type of interest such as a cancer cell, tumor cell, plasma cell, infected cell, or host cell harboring an intracellular pathogen.
  • target biomolecule refers to a biological molecule, commonly a protein or a protein modified by post-translational modifications, such as glycosylation, which is capable of being bound by a binding region to target a protein to a specific cell-type or location within an organism.
  • Extracellular target biomolecules may include various epitopes, including unmodified polypeptides, polypeptides modified by the addition of biochemical functional groups, and glycolipids (see e.g. U.S. Patent 5,091, 178; EP 2431743). It is desirable that an extracellular target biomolecule be endogenously internalized or be readily forced to internalize upon interaction with a protein of the invention.
  • extracellular with regard to modifying a target biomolecule refers to a biomolecule that has at least a portion of its structure exposed to the extracellular environment.
  • Extracellular target biomolecules include cell membrane components, transmembrane spanning proteins, cell membrane-anchored biomolecules, cell-surface-bound biomolecules, and secreted biomolecules.
  • the phrase "physically coupled" when used to describe a target biomolecule means both covalent and/or non- covalent intermolecular interactions that couple the target biomolecule, or a portion thereof, to the outside of a cell, such as a plurality of non-covalent interactions between the target biomolecule and the cell where the energy of each single interaction is on the order of about 1-5 kiloCalories (e.g. electrostatic bonds, hydrogen bonds, Van der Walls interactions, hydrophobic forces, etc.). All integral membrane proteins can be found physically coupled to a cell membrane, as well as peripheral membrane proteins.
  • an extracellular target biomolecule might comprise a transmembrane spanning region, a lipid anchor, a glycolipid anchor, and/or be non-covalently associated (e.g. via non-specific hydrophobic interactions and/or lipid binding interactions) with a factor comprising any one of the foregoing.
  • the binding regions of the proteins of the invention may be designed or selected based on numerous criteria, such as the cell-type specific expression of their target biomolecules and/or the physical localization of their target biomolecules with regard to specific cell types.
  • certain proteins of the present invention comprise binding domains capable of binding cell-surface targets which are expressed exclusively by only one cell-type to the cell surface. This permits the targeted cell-killing of specific cell types with a high preferentiality (at least a 3 -fold cytotoxic effect) over "bystander" cell types that do not express the extracellular target biomolecule.
  • the expression of the target biomolecule of the binding region may be non-exclusive to one cell type if the extracellular target biomolecule is expressed in low enough amounts and/or physically coupled in low amounts with cell types that are not to be targeted.
  • This also permits the targeted cell-killing of specific cell types with a high preferentiality (at least a 3 -fold cytotoxic effect) over "bystander" cell types that do not express significant amounts of the extracellular target biomolecule or are not physically coupled to significant amounts of the extracellular target biomolecule.
  • a targeted cell may be killed using the cytotoxic proteins of the invention under varied conditions of the cell, such as ex vivo, in vitro cultured, or in vivo— including cells in situ in their native locations within a multicellular organism.
  • Extracellular target biomolecules of the binding region of the proteins of the invention may include biomarkers over-proportionately or exclusively present on cancer cells, immune cells, and cells infected with intracellular pathogens, such as viruses, bacteria, fungi, prions, or protozoans.
  • one or more amino acid residues may be mutated, inserted, or deleted in order to increase the enzymatic activity of the de-immunized Shiga toxin effector region.
  • mutating residue-position alanine-231 in StxlA to glutamate increased its enzymatic activity in vitro (Suhan M, Hovde C, Infect Immun 66: 5252-9 (1998)).
  • one or more amino acid residues may be mutated or deleted in order to reduce or eliminate catalytic and/or cytotoxic activity of the de-immunized Shiga toxin effector region.
  • the catalytic and/or cytotoxic activity of the A Subunits of members of the Shiga toxin family may be diminished or eliminated by mutation or truncation as long as at least one amino acid is disrupted in at least one natively positioned epitope region provided in the Examples (Tables 1, 2, 3, 4, and/or 5).
  • the proteins of the invention each comprise a de-immunized Shiga toxin effector region polypeptide which retains at least one Shiga toxin effector function but which may be engineered from a cytotoxic parental molecule to a protein with diminished or abolished cytotoxicity for non-cytotoxic functions, e.g., effectuating cytostasis, delivery of exogenous materials, and/or detection of cell types, by mutating one or more key residues for enzymatic activity.
  • This general structure is modular in that the polypeptides of the invention may be linked to any number of diverse compositions of matter, such as binding regions and/or detection promoting agents for various applications as described herein.
  • the immunogenicity of a molecule (the ability to induce an antibody and/or cell-mediated immune response) can be assessed by observing any immune response (antibody and/or immune cell-mediated) to the molecule after administration to a living organism, such as a chordate. Certain immune responses can be measured, such as the amount and formation of antibodies specifically targeting the administered molecule over time.
  • the presence of antibodies which specifically bind the administered molecule indicate 1) the pre- existence of one or more antibodies which recognized the administered molecule and/or 2) the induction of the de novo formation of one or more antibodies which recognize the administered molecule.
  • the existence of pre-formed anti-molecule antibodies can be determined by investigating pre-administration serum for the presence of anti- molecule antibodies.
  • the induction of de novo anti-"administered molecule" antibody formation can be determined by monitoring post-administration serum for the amount of anti-molecule antibodies generated over time.
  • the amount of antibodies induced in chordates after the administration of a molecule can be measured by comparing the amount of pre-administration, anti-molecule antibodies to the amount of post-administration, anti-molecule antibodies.
  • the amount of anti- "administered molecule" antibodies induced in a chordate after administration is indicative of the general immunogenicity of the molecule and the molecule's ability to induce various immune responses in various chordates, such as inducing increased and diversified anti-molecule antibody production after administration, immune cell-mediated immune responses, molecule neutralizing activities, hypersensitivity reactions, anaphylaxis, anaphylactoid reactions, and other immune responses.
  • the relative immunogenicity of two molecules can be assessed by observing the relative differences in anti-molecule antibodies produced for each molecule respectively after administration of each molecule individually to different organisms.
  • the relative induction of de novo anti-"administered molecule" antibody formation can be determined by measuring the relative differences in post-administration sera for the amount of anti- molecule antibodies generated over time, for each molecule respectively.
  • the amount of antibodies induced in a chordate, such as a mouse, treated with different molecules can be measured with standard ELISA-based assays and used to compare the relative immunogenicity of the different molecules.
  • endoplasmic reticulum retention/retrieval signal motif refers to any member of the KDEL family capable of functioning within a eukaryotic cell to promote subcellular localization of a protein to the endoplasmic reticulum via KDEL receptors.
  • the carboxy -terminal lysine-asparagine-glutamate-leucine (KDEL) sequence is a canonical, endoplasmic reticulum retention and retrieval signal motif for soluble proteins in eukaryotic cells and is recognized by the KDEL receptors (see, Capitani M, Sallese M, FEBS Lett 583: 3863-71 (2009), or review).
  • the KDEL family of signal motifs includes many KDEL-like motifs, such as HDEL, RDEL, WDEL, YDEL, HEEL, KEEL, REEL, KFEL, KIEL, DKEL, KKEL, HNEL, HTEL, KTEL, and HVEL, all of which are found at the carboxy -terminals of proteins which are known to be residents of the lumen of the endoplasmic reticulum of throughout multiple phylogenetic kingdoms
  • the KDEL signal motif family includes at least 46 polypeptide variants shown using synthetic constructs (Raykhel, J Cell Biol 179: 1193-204 (2007)). Additional KDEL signal motifs include ALEDEL,
  • HAEDEL, HLEDEL, KLEDEL, IRSDEL, ERSTEL, and RPSTEL A generalized consensus motif representing the majority of KDEL signal motifs has been described as [KRHQSA]-[DENQ]- E-L (Hulo N et al, Nucleic Acids Res 34: D227-30 (2006)).
  • KDEL receptors Proteins containing KDEL family signal motifs are bound by KDEL receptors distributed throughout the Golgi complex and transported to the endoplasmic reticulum by a microtubule-dependent mechanism for release into the lumen of the endoplasmic reticulum (Griffiths G et al, J Cell Biol 127: 1557- 74 (1994); Miesenb5ck G, Rothman J, J Cell Biol 129: 309-19 (1995)). KDEL receptors dynamically cycle between the Golgi complex and endoplasmic reticulum (Jackson M et al, EMBO J. 9: 3153-62 (1990); Schutze M et al, EMBO J. 13: 1696-1705 (1994)).
  • the members of the KDEL family include synthetic signal motifs able to function within a eukaryotic cell to promote subcellular localization of a protein to the endoplasmic reticulum via KDEL receptors.
  • some members of the KDEL family might not occur in nature or have yet to be observed in nature but have or may be constructed and empirically verified using methods known in the art; see e.g., Raykhel I et al, J Cell Biol 179: 1193-204 (2007).
  • the KDEL-type signal motif is physically located, oriented, or arranged within the protein such that it is on a carboxy -terminal.
  • the specific order or orientation is not fixed for the Shiga toxin effector region and the binding region in relation to each other or the entire protein's N-terminal(s) and C-terminal(s) (see e.g. Figure 1).
  • the binding regions and Shiga toxin effector regions may be directly linked to each other and/or suitably linked to each other via one or more intervening polypeptide sequences, such as with one or more linkers well known in the art.
  • a protein of the invention may further comprise a carboxy-terminal endoplasmic retention/retrieval signal motif, such as KDEL.
  • the general structure of the proteins of the present invention is modular, in that various, diverse binding regions may be used with the same de- immunized Shiga toxin effector region to provide for diverse targeting of various extracellular target biomolecules and thus targeting of cytotoxicity, cytostasis, and/or exogenous material delivery to various diverse cell types.
  • De-immunized Shiga toxin effector regions which are not cytotoxic due to improper subcellular routing may still be useful for delivering exogenous materials into cells.
  • Individual polypeptide and/or protein components of the invention may be suitably linked to each other via one or more linkers well known in the art and/or described herein.
  • Individual polypeptide subcomponents of the binding regions e.g. heavy chain variable regions (VH), light chain variable regions (VL), CDR, and/or ABR regions, may be suitably linked to each other via one or more linkers well known in the art and/or described herein (see e.g.
  • Protein components of the invention may be suitably linked to each other or other polypeptide components of the invention via one or more linkers well known in the art.
  • Peptide components of the invention e.g., KDEL family endoplasmic reticulum retention/retrieval signal motifs, may be suitably linked to another component of the invention via one or more linkers, such as a proteinaceous linker, which are well known in the art.
  • Suitable linkers are generally those which allow each polypeptide component of the invention to fold with a three-dimensional structure very similar to the polypeptide components produced individually without any linker or other component. Suitable linkers include single amino acids, peptides, polypeptides, and linkers lacking any of the aforementioned such as various non- proteinaceous carbon chains, whether branched or cyclic (see e.g. Chen X et al, Adv Drug Deliv Rev 65: 1357-69 (2013)).
  • Suitable linkers may be proteinaceous and comprise one or more amino acids, peptides, and/or polypeptides. Proteinaceous linkers are suitable for both recombinant fusion proteins and chemically linked conjugates.
  • a proteinaceous linker typically has from about 2 to about 50 amino acid residues, such as, e.g., from about 5 to about 30 or from about 6 to about 25 amino acid residues. The length of the linker selected will depend upon a variety of factors, such as, e.g., the desired property or properties for which the linker is being selected (see e.g. Chen X et al, Adv Drug Deliv Rev 65: 1357-69 (2013)).
  • Suitable linkers may be non-proteinaceous, such as, e.g. chemical linkers (see e.g. Dosio F et al, Toxins 3: 848-83 (201 1); Feld J et al, Oncotarget 4: 397- 412 (2013)).
  • Various non-proteinaceous linkers known in the art may be used to link binding regions to the Shiga toxin effector regions, such as linkers commonly used to conjugate immunoglobulin-derived polypeptides to heterologous polypeptides.
  • polypeptide regions may be linked using the functional side chains of their amino acid residues and carbohydrate moieties such as, e.g., a carboxy, amine, sulfhydryl, carboxylic acid, carbonyl, hydroxyl, and/or cyclic ring group.
  • carbohydrate moieties such as, e.g., a carboxy, amine, sulfhydryl, carboxylic acid, carbonyl, hydroxyl, and/or cyclic ring group.
  • disulfide bonds and thioether bonds may be used to link two or more polypeptides (see e.g. Fitzgerald D et al, Bioconjugate Chem 1 : 264-8 (1990); Pasqualucci L et al, Haematologica 80: 546-56 (1995)).
  • non-natural amino acid residues may be used with other functional side chains, such as ketone groups (see e.g.
  • non-proteinaceous chemical linkers include but are not limited to N-succinimidyl (4-iodoacetyl)-aminobenzoate, ⁇ -(N-succinimidyl) thioacetate (SATA), N-succinimidyl-oxycarbonyl-cu-methyl-a-(2-pyridyldithio) toluene (SMPT), N-succinimidyl 4-(2-pyridyldithio)-pentanoate (SPP), succinimidyl 4-(N-maleimidomethyl) cyclohexane carboxylate (SMCC or MCC), sulfosuccinimidyl (4-iodoacetyl)-aminobenzoate, 4-succinimidyl
  • Suitable linkers may include, e.g., protease sensitive, environmental redox potential sensitive, pH sensitive, acid cleavable, photocleavable, and/or heat sensitive linkers (see e.g. Dosio F et al, Toxins 3 : 848-83 (2011); Chen X et al., Adv Drug Deliv Rev 65: 1357-69 (2013); Feld J et al, Oncotarget 4: 397-412 (2013)).
  • Proteinaceous linkers may be chosen for incorporation into recombinant fusion proteins of the invention.
  • linkers typically comprise about 2 to 50 amino acid residues, preferably about 5 to 30 amino acid residues (Argos P, JMol Biol 211: 943-58 (1990); Williamson M, Biochem J 297: 240-60 (1994); George R, Heringa J, Protein Eng 15: 871-9 (2002); Kreitman R, AAPSJ S: E532-51 (2006)).
  • proteinaceous linkers comprise a majority of amino acid residues with polar, uncharged, and/or charged residues, such as, e.g., threonine, proline, glutamine, glycine, and alanine (see e.g. Huston J et al. Proc Natl Acad Sci U.S.A. 85: 5879-83 (1988); Pastan I et al, Annu Rev Med 58: 221-37 (2007); Li J et al, Cell Immunol 118: 85-99 (1989); Cumber A et al.
  • polar, uncharged, and/or charged residues such as, e.g., threonine, proline, glutamine, glycine, and alanine
  • Non-limiting examples of proteinaceous linkers include alanine-serine-glycine-glycine-proline-glutamate (ASGGPE), valine-methionine (VM), alanine- methionine (AM), AM(G2 to 4S) X AM where G is glycine, S is serine, and x is an integer from 1 to 10.
  • Proteinaceous linkers may be selected based upon the properties desired. Proteinaceous linkers may be chosen by the skilled worker with specific features in mind, such as to optimize one or more of the fusion molecule's folding, stability, expression, solubility, pharmacokinetic properties, pharmacodynamic properties, and/or the activity of the fused domains in the context of a fusion construct as compared to the activity of the same domain by itself. For example, proteinaceous linkers may be selected based on flexibility, rigidity, and/or cleavability (see e.g. Chen X et al, Adv Drug Deliv Rev 65: 1357-69 (2013)). The skilled worker may use databases and linker design software tools when choosing linkers.
  • linkers may be chosen to optimize expression (see e.g. Turner D et al, Jlmmunl Methods 205: 43-54 (1997)). Certain linkers may be chosen to promote intermolecular interactions between identical polypeptides or proteins to form homomultimers or different polypeptides or proteins to form heteromultimers. For example, proteinaceous linkers may be selected which allow for desired non-covalent interactions between polypeptide components of the proteins of the invention, such as, e.g., interactions related to the formation dimers and other higher order multimers (see e.g. U.S. 4,946,778).
  • Flexible proteinaceous linkers are often greater than 12 amino acid residues long and rich in small, non-polar amino acid residues, polar amino acid residues, and/or hydrophilic amino acid residues, such as, e.g., glycines, serines, and threonines (see e.g. Bird R et al, Science 242: 423-6 (1988); Friedman P et al, Cancer Res 53: 334-9 (1993); Siegall C et al, J Immunol 152: 2377-84 (1994)). Flexible proteinaceous linkers may be chosen to increase the spatial separation between components and/or to allow for intramolecular interactions between components.
  • GS linkers are known to the skilled worker and are composed of multiple glycines and/or one or more serines, sometimes in repeating units, such as, e.g., (G x S) n , (S x G) n , (GGGGS) n , and (G)n. in which x is 1 to 6 and n is 1 to 30 (see e.g. WO 96/06641).
  • Non- limiting examples of flexible proteinaceous linkers include GKSSGSGSESKS, GSTSGSGKSSEGKG, GSTSGSGKSSEGSGSTKG, GSTSGSGKSSEGKG, GSTSGKPGSGEGSTKG, EGKSSGSESKEF, SRSSG, and SGSSC.
  • Rigid proteinaceous linkers are often stiff alpha-helical structures and rich in proline residues and/or one or more strategically placed prolines (see Chen X et al, Adv Drug Deliv Rev 65: 1357-69 (2013)). Rigid linkers may be chosen to prevent intramolecular interactions between linked components.
  • Suitable linkers may be chosen to allow for in vivo separation of components, such as, e.g., due to cleavage and/or environment-specific instability (see Dosio F et al, Toxins 3: 848-83 (2011); Chen X et al, Adv Drug Deliv Rev 65: 1357-69 (2013)).
  • In vivo cleavable proteinaceous linkers are capable of unlinking by proteolytic processing and/or reducing environments often at a specific site within an organism or inside a certain cell type (see e.g. Doronina S et al, Bioconjug Chem 17: 144-24 (2006); Erickson H et al, Cancer Res 66: 4426-33 (2006)).
  • In vivo cleavable proteinaceous linkers often comprise protease sensitive motifs and/or disulfide bonds formed by one or more cysteine pairs (see e.g. Pietersz G et al., Cancer Res 48: 4469-76 (1998); The J et al, J Immunol Methods 1 10: 101-9 (1998); see Chen X et al, Adv Drug Deliv Rev 65: 1357-69 (2013)).
  • In vivo cleavable proteinaceous linkers can be designed to be sensitive to proteases that exist only at certain locations in an organism, compartments within a cell, and/or become active only under certain physiological or pathological conditions (such as, e.g., proteases with abnormally high levels, proteases overexpressed at certain disease sites, and proteases specifically expressed by a pathogenic microorganism).
  • proteases that exist only at certain locations in an organism, compartments within a cell, and/or become active only under certain physiological or pathological conditions (such as, e.g., proteases with abnormally high levels, proteases overexpressed at certain disease sites, and proteases specifically expressed by a pathogenic microorganism).
  • proteaceous linkers known in the art which are cleaved by proteases present only intracellularly, proteases present only within specific cell types, and proteases present only under pathological conditions like cancer or
  • inflammation such as, e.g., R-x-x-R motif and
  • a linker may be used which comprises one or more protease sensitive sites to provide for cleavage by a protease present within a target cell.
  • a linker may be used which is not cleavable to reduce unwanted toxicity after administration to a vertebrate organism.
  • Suitable linkers may include, e.g., protease sensitive, environmental redox potential sensitive, pH sensitive, acid cleavable, photocleavable, and/or heat sensitive linkers, whether proteinaceous or non-proteinaceous (see Chen X et al, Adv Drug Deliv Rev 65: 1357-69 (2013)).
  • Suitable cleavable linkers may include linkers comprising cleavable groups which are known in the art such as, e.g., Zarling D et al, J Immunol 124: 913-20 (1980); Jung S, Moroi M, Biochem Biophys Acta 761 : 152-62 (1983); Bouizar Z et al, Eur J Biochem 155: 141-7 (1986); Park L et al, J Biol Chem 261: 205-10 (1986); Browning J, Ribolini A, J Immunol 143: 1859-67 (1989); Joshi S, Burrows R, J Biol Chem 265: 14518-25 (1990)).
  • Suitable linkers may include pH sensitive linkers.
  • certain suitable linkers may be chosen for their instability in lower pH environments to provide for dissociation inside a subcellular compartment of a target cell.
  • linkers that comprise one or more trityl groups, derivatized trityl groups, bismaleimideothoxy propane groups, adipic acid dihydrazide groups, and/or acid labile transferrin groups may provide for release of components of the proteins of the invention, e.g. a polypeptide component, in environments with specific pH ranges (see e.g.
  • Certain linkers may be chosen which are cleaved in pH ranges corresponding to physiological pH differences between tissues, such as, e.g., the pH of tumor tissue is lower than in healthy tissues (see e.g. U.S. 5,612,474).
  • Photocleavable linkers are linkers that are cleaved upon exposure to electromagnetic radiation of certain wavelength ranges, such as light in the visible range (see e.g. Goldmacher V et al, Bioconj Chem 3: 104-7 (1992)). Photocleavable linkers may be used to release a component of a protein of the invention, e.g. a polypeptide component, upon exposure to light of certain wavelengths.
  • Photocleavable linkers include a nitrobenzyl group as a photocleavable protective group for cysteine,
  • Photocleavable linkers may have particular uses in linking components to form proteins of the invention designed for treating diseases, disorders, and conditions that can be exposed to light using fiber optics.
  • a binding region is linked to a Shiga toxin effector region using any number of means known to the skilled worker, including both covalent and noncovalent linkages (see e.g. Chen X et al, Adv Drug Deliv Rev 65: 1357-69 (2013); Behrens C, Liu B, MAbs 6: 46-53 (2014).
  • the protein comprises a binding region which is a scFv with a linker connecting a heavy chain variable (VH) domain and a light chain variable (VL) domain.
  • VH heavy chain variable
  • VL light chain variable
  • linkers known in the art suitable for this purpose, such as, e.g., the 15- residue (Gly4Ser)3 peptide.
  • Suitable scFv linkers which may be used in forming non-covalent multivalent structures include GGS, GGGS, GGGGS,
  • Suitable methods for linkage of the components of the proteins of the invention may be by any method presently known in the art for accomplishing such, so long as the attachment does not substantially impede the binding capability of the binding regions, the cellular internalization of the protein, and/or desired toxin effector functions of the Shiga toxin effector region as measured by an appropriate assay, including assays described herein.
  • the specific order or orientation is not fixed for the Shiga toxin effector region and the cell-targeting binding region in relation to each other or the entire protein (see e.g. Figure 1).
  • the components of the polypeptides and proteins of the invention may be arranged in any order provided that the desired activities of the binding region and the Shiga toxin effector region are not eliminated.
  • the binding regions, Shiga toxin effector regions (which may be cytotoxic and/or harbor one or more mutations reducing or eliminating catalytic activity and/or cytotoxicity), and endoplasmic reticulum retention/retrieval signal motif may be directly linked to each other and/or suitably linked to each other via one or more intervening polypeptide sequences, such as with one or more linkers well known in the art and/or described herein.
  • any amino acid in the provided epitope regions may be disrupted by various means, such as, e.g., deletion, insertion, inversion, rearrangement, substitution, and chemical modification of side chains.
  • disrupting certain amino acids and polypeptide regions using certain disruptions are more likely to successfully reduce antigenicity and/or immunogenicity while retaining a Shiga toxin effector function.
  • terminal truncations and internal amino acid substitutions are preferred because they maintain the overall amino acid spacing of the Shiga toxin effector region and thus are more likely to maintain Shiga toxin effector functions.
  • the polypeptides comprise the de-immunized Shiga toxin effector region comprising or consisting essentially of amino acids 75 to 251 of SLT-1A (SEQ ID O: l), StxA (SEQ ID NO: 2), and/or SLT-2A (SEQ ID NO:3) wherein at least one amino acid is disrupted in the natively positioned epitope regions provided in the Examples (Tables 1, 2, 3, 4, and/or 5).
  • polypeptides comprising a de-immunized Shiga toxin effector region derived from amino acids 1 to 241 of SLT-1A (SEQ ID NO: l), StxA (SEQ ID NO:2), and/or SLT- 2A (SEQ ID NO:3) wherein at least one amino acid is disrupted in the natively positioned epitope regions provided in the Examples (Tables 1, 2, 3, 4, and/or 5).
  • polypeptides comprising a de-immunized Shiga toxin effector region which is derived from amino acids 1 to 251 of SLT-1A (SEQ ID NO: 1), StxA (SEQ ID NO:2), and/or SLT-2A (SEQ ID NO:3) wherein at least one amino acid is disrupted in the natively positioned epitope regions provided in the Examples (Tables 1, 2, 3, 4, and/or 5).
  • polypeptides comprising a de-immunized Shiga toxin effector region which is derived from amino acids 1 to 261 of SLT-1A (SEQ ID NO: l), StxA (SEQ ID NO: 2), and/or SLT-2A (SEQ ID NO:3) wherein at least one amino acid is disrupted in the natively positioned epitope regions provided in the Examples (Tables 1, 2, 3, 4, and/or 5).
  • substitute amino acid residues are predicted to be the most likely to reduce the antigenicity and/or immunogenicity of an epitope— G, D, E, S, T, R, K, and H. Except for glycine, these residues all represent polar and/or charged residues.
  • amino acids A, G, V, L, I, P, C, M, F, S, D, N, Q, H, and K are predicted to be the most likely to reduce antigenicity and/or immunogenicity while retaining a significant Shiga toxin effector function depending on the amino acid substituted for.
  • the substitution should change a polar and/or charged amino acid residue to a non-polar and uncharged residue.
  • alanine is generally an acceptable substitution for any amino acid residue, and, for glycine residues, alanine is the preferred choice.
  • Serine is generally only an acceptable substitution for glutamate residues. Aspartate is generally only an acceptable substitution for glutamate residues. Lysine is generally only an acceptable substitution for arginine residues. Glutamine is generally only an acceptable substitution for glutamate, lysine, or arginine residues. Histidine is generally only an acceptable substitution for lysine and arginine residues.
  • the substitute amino acid might be more likely to preserve Shiga toxin effector function(s) if it resembles the amino acid substituted for, such as, e.g., a nonpolar and/or uncharged residue of similar size substituted for a polar and/or charged residue.
  • a Shiga toxin effector region polypeptide of the invention may comprise similar conservative amino acid substitutions such as, e.g., Kl to A, G, V, L, I, F, M and H; T4 to A, G, V, L, I, F, M, and S; S8 to A, G, V, I, L, F, and M; T9 to A, G, V, I, L, F, M, and S; S9 to A, G, V, L, I, F, and M; Kl 1 to A, G, V, L, I, F, M and H; S33 to A, G, V, L, I, F, and M; S45 to A, G, V, L, I, F, and M; T45 to A, G, V, L, I, F, and M; D47 to A, G, V, L,
  • a Shiga toxin effector region polypeptide of the invention may comprise one or more epitopes disrupted by substitutions such that side chain charge is removed, polarity is removed, and/or side chain length is reduced such as, e.g., substituting the appropriate amino acid selected from the following group A, G, V, L, I, P, C, M, F, S, D, N, Q, H, or K for the amino acid residue at position 1 of SEQ ID NO: 1 or SEQ ID NO:2; 4 of SEQ ID NO: l, SEQ ID NO:2, or SEQ ID NO:3; 8 of SEQ ID NO: 1, SEQ ID NO:2, or SEQ ID NO:3; 9 of SEQ ID NO: 1, SEQ ID NO:2, or SEQ ID NO:3; 11 of SEQ ID NO:l,
  • a Shiga toxin effector region polypeptide of the invention may comprise one or more of the following amino acid substitutions: Kl to A, G, V, L, I, F, M and H; T4 to A, G, V, L, I, F, M, and S; S8 to A, G, V, I, L, F, and M; T9 to A, G, V, I, L, F, M, and S; S9 to A, G, V, L, I, F, and M; Kl 1 to A, G, V, L, I, F, M and H; S33 to A, G, V, L, I, F, and M; S45 to A, G, V, L, I, F, and M; T45 to A, G, V, L, I, F, and M; D47 to A, G, V, L, I, F, S, and Q; N48 to A, G, V, L, and M; L49 to A or G; D53 to A, G, V, L, L, I
  • any amino acid substitution in one epitope region of a Shiga toxin effector polypeptide which disrupts an epitope while retaining significant Shiga toxin effector function is combinable with any other amino acid substitution in the same or a different epitope region which disrupts an epitope while retaining significant Shiga toxin effector function to form a de-immunized Shiga toxin effector polypeptide with multiple epitope regions disrupted while still retaining a significant level of Shiga toxin effector function.
  • a Shiga toxin effector region polypeptide of the invention may comprise one or more of the following combinations: KIM may be combined with S8I, T9I, Kl 1A, S33I, S45I, T45I, D53A, R55A, D58A, D58F, P59A, E60I, E60R, E61A, G62A, D94A, S96I, G110A, G147A, T180G, T181I, D183A, D184A, D184F, S186A, G187A, R188A, S189A, R204A, R205A,
  • S8I may be combined with KIM, T9I, Kl lA, S45I, T45I, D53A, R55A, D58A, D58F, P59A, E60I, E60R, E61A, G62A, D94A, S96I, G110A, G147A, T180G, T181I, D183A, D184A, D184F, S186A, G187A, R188A, S189A, R204A, R205A, S247I, D264A, G264A, G265A, and/or T286I; T9I may be combined with KIM, S8I, Kl 1A, S45I, T45I, D53A, R55A, D58A, D58F, P59A, E60I, E60R, E61A, G62A, D94A, S96I, G110A, G147A
  • S33I may be combined with KIM, S8I, T9I, Kl lA, S45I, T45I, D53A, R55A, D58A, D58F, P59A, E60I, E60R, E61A, G62A, D94A, S96I, G110A, G147A, T180G, T181I, D183A, D184A, D184F, S186A, G187A, R188A, S189A, R204A, R205A, S247I, D264A, G264A, G265A, and/or T286I; S45V or S45I may be combined with KIM, S8I, T9I, Kl lA, S33I, D53A, R55A, D58A, D58F, P59A, E60I, E60R, E61A, G62A, D94
  • D58A or D58F may be combined with KIM, S8I, T9I, K11A, S33I, S45I, T45I, D53A, R55A, P59A, E60I, E60R, E61A, G62A, Gl lOA, D94A, S96I, G147A, T180G, T181I, D183A, D184A, D184F, S186A, G187A, R188A, S189A, R204A, R205A, S247I, D264A, G264A, G265A, and/or T286I; R55A may be combined with KIM, S8I, T9I,
  • E60I or E60A may be combined with KIM, S8I, T9I, Kl 1A, S45I, T45I, D53A, R55A, D58A, D58F, P59A, E61A, G62A, D94A, S96I, Gl lOA, G147A, T180G, T181I, D183A, D184A, D184F, S186A, G187A, R188A, S189A, R204A, R205A, S247I, D264A, G264A, G265A, and/or T286I; E61A may be combined with KIM, S8I, T9I, K11A, S45I, T45I, D53A, R55A, D58A, D58F, P59A, E60I, E60R, G62A, D94A, S96I, Gl
  • D183A may be combined with KIM, S8I, T9I, K11A, S33I, S45I, T45I, D53A, R55A, D58A, D58F, P59A, E60I, E60R, E61A, G62A, D94A, S96I, G110A, G147A, T180G, T181I, D184A, D184F, S186A, G187A, R188A, S189A, R204A, R205A, S247I, D264A, G264A, G265A, and/or T286I; D184A or D184F may be combined with KIM, S8I, T9I, K11A, S33I, S45I, T45I, D53A, R55A, D58A, D58F, P59A, E60I, E60R, E61A, G62A, D94
  • D264A may be combined with KIM, S8I, T9I, K11A, S45I, T45I, D53A, R55A, D58A, D58F, P59A, E60I, E60R, E61A, G62A, D94A, S96I, G110A, G147A, T180G, T181I, D183A, D184A, D184F, S186A, G187A, R188A, S189A, R204A, R205A, S247I, G264A, G265A, and/or T286I; G264A may be combined with KIM, S8I, T9I, Kl 1A, S45I, T45I, D53A, R55A, D58A, D58F, P59A, E60I, E60R, E61A, G62A, D94A, S96I, G110A, G147
  • Proteins of the invention comprise de- immunized Shiga toxin effector regions derived from the A Subunits of members of the Shiga toxin family linked to binding regions which can bind specifically to at least one extracellular target biomolecule in physical association with a cell, such as a target biomolecule expressed on the surface of a cell.
  • This general structure is modular in that any number of diverse cell-targeting binding regions may be linked to the de-immunized Shiga toxin effector region polypeptides of the invention.
  • the proteins comprise a binding region derived from an immunoglobulin-type polypeptide selected for specific and high-affinity binding to a surface antigen on the cell surface of a cancer cell, where the antigen is restricted in expression to cancer cells (see Glokler J et al, Molecules 15: 2478-90 (2010); Liu Y et al, Lab Chip 9: 1033-6 (2009).
  • the binding region is selected for specific and high-affinity binding to a surface antigen on the cell surface of a cancer cell, where the antigen is over-expressed or preferentially expressed by cancer cells as compared to non-cancer cells.
  • Some representative target biomolecules include, but are not limited to, the following enumerated targets associated with cancers and/or specific immune cell types.
  • binding regions that recognize epitopes associated with cancer cells exist in the prior art, such as binding regions that target annexin Al, B3 melanoma antigen, B4 melanoma antigen, CD2, CD3,
  • CD4 B-lymphocyte antigen protein CD20
  • CD22 CD25
  • CD25 interleukin-2 receptor IL2R
  • CD30 TNFRSF8
  • CD38 cyclic ADP ribose hydrolase
  • CD40, CD44 hyaluronan receptor
  • ITGAV CD51
  • CD66 CD71
  • CD73 CD74
  • CD74 HLA-DR antigens-associated invariant chain
  • CD79 CD98
  • endoglin END, CD 105
  • CD 106 VCAM-1
  • chemokine receptor type 4 CD200
  • CD221) mucin 1 (MUC1, CD227), basal cell adhesion molecule (B-CAM, CD239), CD248 (endosialin, TEM1), tumor necrosis factor receptor 10b (TNFRSF10B, CD262), tumor necrosis factor receptor 13B (TNFRSF 13B, TACI, CD276), vascular endothelial growth factor receptor 2 (KDR, CD309), epithelial cell adhesion molecule (EpCAM, CD326), human epidermal growth factor receptor 2 (HER2, Neu, ErbB2, CD340), cancer antigen 15-3 (CA15-3), cancer antigen 19-9 (CA 19-9), cancer antigen 125 (CA125, MUC16), CA242, carcinoembryonic antigen-related cell adhesion molecules (e.g.
  • CEACAM3 (CD66d) and CEACAM5), carcinoembryonic antigen protein (CEA), chondroitin sulfate proteoglycan 4 (CSP4, MCSP, NG2), CTLA4, DLL4, epidermal growth factor receptor (EGFR, ErbBl), folate receptor (FOLR), G-28, ganglioside GD2, ganglioside GD3, HLA-DrlO, HLA-DRB, human epidermal growth factor receptor 1 (HER1), Ephrin type-B receptor 2 (EphB2), epithelial cell adhesion molecule (EpCAM), fibroblast activation protein (FAP/seprase), insulin-like growth factor 1 receptor (IGF1R), interleukin 2 receptor (IL-2R), interleukin 6 receptor (IL-6R), integrins alpha-V beta-3 ( ⁇ 3), integrins alpha-V beta-5 ( ⁇ 5), integrins alpha-5 beta-1 ( ⁇ ), L6, MPG,
  • PVRL4 protease-activated-receptors (such as PARI), prostate-specific membrane antigen protein (PSMA), trophoblast glycoprotein (TPGB), and tumor-associated calcium signal transducers (TACSTDs)
  • PARI protease-activated-receptors
  • PSMA prostate-specific membrane antigen protein
  • TPGB trophoblast glycoprotein
  • TACSTDs tumor-associated calcium signal transducers
  • BAGE proteins B melanoma antigens
  • basal cell adhesion molecules BCAMs or Lutheran blood group glycoproteins
  • bladder tumor antigen BTA
  • cancer-testis antigen NY-ESO-1 cancer-testis antigen LAGE proteins
  • CD 19 B- lymphocyte antigen protein CD 19
  • CD21 complement receptor-2 or complement 3d receptor
  • CD26 dipeptidyl peptidase-4, DPP4, or adenosine deaminase complexing protein 2
  • CD33 sialic acid-binding immunoglobulin- type lectin-3
  • CD52 CAMPATH-1 antigen
  • CD56 CS1 (SLAM family number 7 or SLAMF7)
  • cell surface A33 antigen protein gpA33
  • Epstein-Barr Virus antigen proteins GAGE/PAGE proteins (melanoma associated cancer/testis antigens)
  • hexA33 Epstein-Barr Virus antigen proteins
  • GAGE/PAGE proteins melanoma associated cancer/testis antigen
  • Examples of other target biomolecules which are strongly associated with cancer cells are carbonic anhydrase IX (CA9/CAIX), Claudin proteins (CLDN3, CLDN4), ephrin type-A receptor 3 (EphA3), folate binding proteins (FBP), ganglioside GM2, insulin-like growth factor receptors, integrins (such as CDl la- c), receptor activator of nuclear factor kappa B (RANK), receptor tyrosine- protein kinase erB-3, tumor necrosis factor receptor 10A (TRAIL-R1/DR4), tumor necrosis factor receptor 10B (TRAIL-R2), Tenascin C, and CD64 (FcyRI) (see Hough C et al, Cancer Res 60: 6281-7 (2000); Thepen T et al, Nat Biotechnol 18: 48-51 (2000); Pastan I et al, Nat Rev Cancer 6: 559-65 (2006); Pastan, Annu Rev Med
  • target biomolecules such as ADAM metalloproteinases (e.g. ADAM-9, ADAM- 10, ADAM- 12, ADAM- 15, ADAM- 17), ADP-ribosyltransferases (ART1, ART4), antigen F4/80, bone marrow stroma antigens (BST1, BST2), break point cluster region-c-abl oncogene (BCR-ABL) proteins, C3aR (complement component 3a receptors), CD7, CD 13, CD 14, CD 15 (Lewis X or stage-specific embryonic antigen 1), CD23 (FC epsilon RII), CD49d, CD53, CD54 (intercellular adhesion molecule 1), CD63 (tetraspanin), CD69, CD80, CD86, CD88 (complement component 5a receptor 1), CDl 15 (colony stimulating factor 1 receptor), CD123 (interleukin-3 receptor), CD 129 (interleukin 9 receptor),
  • ADAM metalloproteinases e.g.
  • HAAH asparaginyl beta-hydroxylase
  • LPGAT1/IAA0205 lysophosphatidlglycerol acyltransferase 1
  • LAMPs lysosome- associated membrane proteins
  • CD 107 melanocyte protein PMEL (gplOO), myeloid-related protein- 14 (mrp-14), receptor tyrosine-protein kinase erbB-3, SART proteins, scavenger receptors (such as CD64 and CD68), Siglecs (sialic acid-binding immunoglobulin-type lectins), syndecans (such as SDC1 or CD138), tyrosinase, tyrosinease-related protein 1 (TRP-1), tyrosinease- related protein 2 (TRP-2), tyrosinase associated antigen (TAA), APO-3, BCMA, CD2, CD3, CD4, CD8, CD18, CD
  • the binding region comprises or consists essentially of an immunoglobulin-type polypeptide selected for specific and high-affinity binding to the cellular surface of a cell type of the immune system.
  • immunoglobulin-type binding domains are known that bind to CD1, CD2, CD3, CD4, CD5, CD6, CD7, CD8, CD9, CD10, CD11, CD12, CD13, CD14, CD15, CD16, CD17, CD18, CD19, CD20, CD21, CD22, CD23, CD24, CD25, CD26, CD27, CD28, CD29, CD30, CD31, CD33, CD34, CD35, CD36, CD37, CD38, CD40, CD41, CD56, CD61, CD62, CD66, CD95, CD117, CD 123, CD235, CD 146, CD326, interleukin-2 receptor (IL-2R), receptor activator of nuclear factor kappa B (RANKL), SLAM-associated protein (SAP), and TNFSF18
  • IL-2R interleuk
  • the de-immunized cytotoxic protein comprises or consists essentially of amino acids of SEQ ID NO:53, SEQ ID NO:54, SEQ ID NO:55, or SEQ ID NO:56.
  • These de-immunized CD20-binding cytotoxic protein embodiments may be used to treat and/or diagnosis bone cancer, leukemia, lymphoma, melanoma, myeloma, amyloidosis, ankylosing spondylitis, asthma, Crohn's disease, diabetes, graft rejection, graft-versus-host disease, Hashimoto's thyroiditis, hemolytic uremic syndrome, HIV-related diseases, lupus erythematosus, multiple sclerosis, polyarteritis, psoriasis, psoriatic arthritis, rheumatoid arthritis, scleroderma, septic shock, Sjorgren's syndrome, ulcerative colitis, and/or vasculitis.
  • the de-immunized cytotoxic protein comprises or consists essentially of amino acids of SEQ ID NO:57, SEQ ID NO:58, or SEQ ID NO:59.
  • These de-immunized HER-2-binding cytotoxic protein embodiments may be used to treat and/or diagnosis of breast cancer, cervical cancer, head- neck cancer (e.g. oropharynx), gastrointestinal cancer (e.g. esophageal and colorectal), kidney-urinary tract cancer (e.g. bladder), lung/pleura cancer, and ovarian cancer.
  • the binding region comprises or consists essentially of a ligand selected for targeting an extracellular receptor.
  • ligands include, but are not limited to, the following bone morphogenetic proteins and activin membrane-bound inhibitor BAMBI (also known as TGFBR), CD137L (also known as 4- IBB), decoy receptor 3 DcR3 (also known as TR6 and TNFRSF6B), and the tumor necrosis factor TWEAK (also known as TNFSF12 and AP03L).
  • BAMBI also known as TGFBR
  • CD137L also known as 4- IBB
  • decoy receptor 3 DcR3 also known as TR6 and TNFRSF6B
  • TWEAK tumor necrosis factor
  • De-immunized Shiga toxin effector regions which become non-toxic after epitope disruption may still be useful for delivering exogenous materials into cells.
  • De-immunized Shiga toxin effector regions which retain only a significant level of the Shiga toxin function of catalytic activity are still useful as enzymatically active, de- immunized components of molecules.
  • any binding region comprising a polypeptide that binds to a target biomolecule, preferably expressed on a cell surface, with a dissociation constant of 10 "5 to 10 "12 moles per liter, preferably less than 200 nM, may be substituted for use in making molecules of the invention (e.g. de- immunized Shiga toxin effector polypeptides and cytotoxic proteins) and methods of the invention.
  • polypeptides and proteins of the invention have improved usefulness for administration to mammalian species as either a therapeutic and/or diagnostic agent because of the reduced likelihood of producing undesired immune responses in mammals.
  • the desired biological functions of the original Shiga toxin effector regions were preserved after the B-cell epitope(s) was disrupted.
  • B-cell epitopes often coincide or overlap with epitopes of mature CD4+ T-cells, thus the disruption of a B-cell epitope often simultaneously disrupts a CD4+ T-cell epitope.
  • the various de-immunized Shiga toxin effector polypeptides of the invention might differ in their antigenicity profiles when administered to various mammals, but are expected to have reduced antigenicity and/or immunogenicity. It is not necessary to completely eliminate all immunogenicity from a Shiga toxin derived polypeptide in order to improve its use in medical applications involving administration to a mammal (see Nagata, Adv Drug Deliv Rev 61 : 977- 85 (2009)). The modification of only a few dominant amino acids in a therapeutic protein can greatly reduce its antigenicity and/or immunogenicity without perturbing the protein's overall stability, structure, and function.
  • Shiga toxin effector polypeptide regions with disruptions in more immunogenic B-cell epitopes are expected to be more advantageous for administration to mammals when it is desirable to avoid unwanted B-cell and/or CD4+ T-cell immune responses.
  • the present invention provides various de-immunized Shiga toxin effector polypeptides which may be used as components of various compositions of matter, such as cell-targeted cytotoxic proteins and diagnostic compositions.
  • the de-immunized Shiga toxin effector polypeptides have uses as components of various protein therapeutics, such as, e.g. immunotoxins and ligand-toxin fusions, for the targeted killing of specific cell types for the treatment of a variety of diseases, including cancers, immune disorders, and microbial infections.
  • the present invention also provides various cytotoxic proteins comprising de-immunized Shiga toxin effector regions functionally associated with binding regions to effectuate cell targeting such that the cytotoxic proteins selectively kill, inhibit the growth of, deliver exogenous material to and/or detect specific cell types.
  • the binding regions of the proteins of the invention are capable of binding specifically to at least one extracellular target biomolecule in physical association with a cell, such as a target biomolecule expressed on the surface of a cell.
  • the linking of cell targeting binding regions with de- immunized Shiga toxin effector region polypeptides enables the engineering of cell-type specific targeting of the potent Shiga toxin cytotoxicity and/or cytostasis.
  • the proteins of the invention are capable of binding extracellular target biomolecules associated with the cell surface of particular cell types and entering those cells. Once internalized within a targeted cell type, certain embodiments of the proteins of the invention are capable of routing an enzymatically active, cytotoxic, Shiga toxin effector polypeptide fragment into the cytosol of the target cell. Once in the cytosol of a targeted cell type, certain embodiments of the cytotoxic proteins of the invention are capable of enzymatically inactivating ribosomes and eventually killing the cell.
  • nontoxic variants of the proteins of the invention may be used to deliver additional exogenous materials into target cells, such as peptides, polypeptides, proteins, polynucleotides, and detection promoting agents.
  • target cells such as peptides, polypeptides, proteins, polynucleotides, and detection promoting agents.
  • This system is modular, in that any number of diverse binding regions can be used to target this potent cytotoxicity to various, diverse cell types.
  • cytotoxic proteins designed using de-immunized Shiga toxin effector regions can show potent cell-kill activity.
  • the A Subunits of members of the Shiga toxin family comprise enzymatic domains capable of killing a eukaryotic cell once in the cell's cytosol.
  • the disruption of B-cell epitopes did not significantly alter the cytotoxic mechanism of certain Shiga toxin effector regions of the invention.
  • the de-immunized cytotoxic proteins of the invention maintain potent cytotoxicity while reducing the likelihood of certain immune responses when administered to a mammal.
  • the cytotoxic protein upon contacting a cell physically coupled with an extracellular target biomolecule of the binding region of a cytotoxic protein of the invention (target+ cell), the cytotoxic protein is capable of causing death of the cell.
  • Cell kill may be accomplished using a cytotoxic protein of the invention under varied conditions of target cells, such as an ex vivo manipulated target cell, a target cell cultured in vitro, a target cell within a tissue sample cultured in vitro, or a target cell in vivo.
  • this potent cell-kill activity can be restricted to preferentially killing selected cell types.
  • the protein upon administration of the protein of the invention to a mixture of cell types, is capable of selectively killing those cells which are physically coupled with an extracellular target biomolecule compared to cell types not physically coupled with an extracellular target biomolecule.
  • members of the Shiga toxin family are adapted for killing eukaryotic cells, cytotoxic proteins designed using Shiga toxin effector regions can show potent cytotoxic activity.
  • this potent cell kill activity can be restricted to killing only those cell types desired to be targeted by their physical association with a target biomolecule of the chosen binding regions.
  • the cytotoxic protein of the invention is capable of selectively or preferentially causing the death of a specific cell type within a mixture of two or more different cell types. This enables the targeted cytotoxic activity to specific cell types with a high preferentiality, such as a 3 -fold cytotoxic effect, over "bystander" cell types that do not express the target biomolecule.
  • the expression of the target biomolecule of the binding region may be non-exclusive to one cell type if the target biomolecule is expressed in low enough amounts and/or physically coupled in low amounts with cell types that are not to be targeted.
  • the cytotoxic protein upon administration of the cytotoxic protein to two different populations of cell types, is capable of causing cell death as defined by the half-maximal cytotoxic concentration (CD50) on a population of target cells, whose members express an extracellular target biomolecule of the binding region of the cytotoxic protein, at a dose at least three-times lower than the CD50 dose of the same cytotoxic protein to a population of cells whose members do not express an extracellular target biomolecule of the binding region of the cytotoxic protein.
  • CD50 half-maximal cytotoxic concentration
  • the cytotoxic activity toward populations of cell types physically coupled with an extracellular target biomolecule is at least 3- fold higher than the cytotoxic activity toward populations of cell types not physically coupled with any extracellular target biomolecule of the binding region.
  • selective cytotoxicity may be quantified in terms of the ratio (a/b) of (a) cytotoxicity towards a population of cells of a specific cell type physically coupled with a target biomolecule of the binding region to (b) cytotoxicity towards a population of cells of a cell type not physically coupled with a target biomolecule of the binding region.
  • the cytotoxicity ratio is indicative of selective cytotoxicity which is at least 3-fold, 5-fold, 10-fold, 15-fold, 20-fold, 25-fold, 30-fold, 40-fold, 50- fold, 75-fold, 100-fold, 250-fold, 500-fold, 750-fold, or 1000-fold higher for populations of cells or cell types physically coupled with a target biomolecule of the binding region compared to populations of cells or cell types not physically coupled with a target biomolecule of the binding region.
  • This preferential cell-killing function allows a targeted cell to be killed by certain cytotoxic proteins of the invention under varied conditions and in the presence of non-targeted bystander cells, such as ex vivo manipulated mixtures of cell types, in vitro cultured tissues with mixtures of cell types, or in vivo in the presence of multiple cell types (e.g. in situ or in its native location within a multicellular organism).
  • proteins of the invention optionally may be used for information gathering and diagnostic functions. Futher, non-toxic variants of the cytotoxic proteins of the invention, or optionally toxic variants, may be used to deliver additional exogenous materials to and/or label the interiors of cells physically coupled with an extracellular target biomolecule of the cytotoxic protein. Various types of cells and/or cell populations which express target biomolecules to at least one cellular surface may be targeted by the proteins of the invention for receiving exogenous materials.
  • the functional components of the present invention are modular, in that various Shiga toxin effector regions and additional exogenous materials may be linked to various binding regions to provide diverse applications, such as noninvasive in vivo imaging of tumor cells.
  • proteins of the invention are capable of entering cells physically coupled with an extracellular target biomolecule recognized by its binding region
  • certain embodiments of the proteins of the invention may be used to deliver additional exogenous materials into the interior of targeted cell types.
  • the entire protein of the invention is an exogenous material which will enter the cell; thus, the
  • exogenous materials are heterologous materials linked to but other than the core cytotoxic protein itself.
  • De-immunized Shiga toxin effector regions which become non-toxic after epitope disruption may still be useful for delivering exogenous materials into cells (e.g. R179A).
  • Additional exogenous material refers to one or more molecules, often not generally present within a native target cell, where the proteins of the present invention can be used to specifically transport such material to the interior of a cell.
  • additional exogenous materials are peptides, polypeptides, proteins, polynucleotides, small molecule chemotherapeutic agents, and detection promoting agents.
  • the additional exogenous material comprises a protein or polypeptide comprising an enzyme.
  • the additional exogenous material is a nucleic acid, such as, e.g. a ribonucleic acid that functions as a small inhibiting RNA (siRNA) or microRNA (miRNA).
  • the additional exogenous material is an antigen, such as antigens derived from bacterial proteins, viral proteins, proteins mutated in cancer, proteins aberrantly expressed in cancer, or T-cell complementary determining regions.
  • exogenous materials include antigens, such as those characteristic of antigen-presenting cells infected by bacteria, and T-cell complementary determining regions capable of functioning as exogenous antigens.
  • Additional examples of exogenous materials include polypeptides and proteins larger than an antigenic peptide, such as enzymes. Exogenous materials comprising polypeptides or proteins may optionally comprise one or more antigens whether known or unknown to the skilled worker.
  • Certain proteins of the invention have uses in the in vitro and/or in vivo detection of specific cells, cell types, and/or cell populations.
  • the proteins described herein are used for both diagnosis and treatment, or for diagnosis alone.
  • the cytotoxic protein variant which incorporates a detection promoting agent for diagnosis may be rendered nontoxic by catalytic inactivation of a Shiga toxin effector region via one or more amino acid substitutions, including exemplary substitutions described herein.
  • Nontoxic forms of the cytotoxic proteins of the invention that are conjugated to detection promoting agents optionally may be used for diagnostic functions, such as for companion diagnostics used in conjunction with a therapeutic regimen comprising the same or a related binding region.
  • diagnostic embodiments of the proteins of the invention may be used for information gathering via various imaging techniques and assays known in the art.
  • diagnostic embodiments of the proteins of the invention may be used for information gathering via imaging of intracellular organelles (e.g. endocytotic, Golgi, endoplasmic reticulum, and cytosolic compartments) of individual cancer cells, immune cells, or infected cells in a patient or biopsy sample.
  • intracellular organelles e.g. endocytotic, Golgi, endoplasmic reticulum, and cytosolic compartments
  • Various types of information may be gathered using the diagnostic embodiments of the proteins of the invention whether for diagnostic uses or other uses. This information may be useful, for example, in diagnosing neoplastic cell types, determining therapeutic susceptibilities of a patient's disease, assaying the progression of antineoplastic therapies over time, assaying the progression of immunomodulatory therapies over time, assaying the progression of antimicrobial therapies over time, evaluating the presence of infected cells in transplantation materials, evaluating the presence of unwanted cell types in transplantation materials, and/or evaluating the presence of residual tumor cells after surgical excision of a tumor mass.
  • subpopulations of patients might be ascertained using information gathered using the diagnostic variants of the proteins of the invention, and then individual patients could be categorized into subpopulations based on their unique characteristic(s) revealed using those diagnostic embodiments.
  • the effectiveness of specific pharmaceuticals or therapies might be one type of criterion used to define a patient subpopulation.
  • a nontoxic diagnostic variant of a particular cytotoxic protein of the invention may be used to differentiate which patients are in a class or subpopulation of patients predicted to respond positively to a cytotoxic variant of the same protein of the invention. Accordingly, associated methods for patient identification, patient stratification, and diagnosis using de-immunized proteins of the invention, including non-toxic variants of cytotoxic proteins of the invention, are considered to be within the scope of the present invention.
  • the polypeptides of the invention have uses as biased immunization and/or vaccination materials for driving the elicitation of immune responses to specific epitopes in the presence of a de-immunized Shiga toxin effector region polypeptide of the invention. Infections by Shiga toxin producing
  • Shiga toxin producing bacteria are the leading cause of hemolytic uremic syndrome (HUS) and Shigellosis, as well as the associated conditions such as hemorrhagic colitis and diarrhea (see Karmali M, Mol Biotechnol 26: 1 17-22 (2004)).
  • Shiga toxins are classified by the U.S. Centers for Disease Control and Prevention (CDC) as category B biothreat agents for their potential to be used as a bioweapon.
  • Mammalian antibodies elicited during immune responses to a Shiga holotoxin or Shiga toxin subunit may be either neutralizing or non-neutralizing depending on the epitope. Furthermore, antibodies recognizing Shiga toxins may have different neutralizing effects depending on which Shiga toxin subunit comprises the epitope of the antibody (Krautz-Peterson G et al, Infect Immun 76: 1931-9 (2008)).
  • Certain polypeptides of the invention are thus useful in methods to artificially drive mammalian immune responses away from certain epitope regions, such as, e.g., which elicit undesirable non-neutralizing antibodies and towards other epitopes, such as, e.g., which elicit desirable neutralizing and/or protective antibodies.
  • Certain polypeptides of the invention have uses as biased immunization and/or vaccination materials in methods for reducing and/or eliminating the antigenicity and/or immunogenicity of specific epitopes while permitting the elicitation of immune responses to undisrupted, native epitopes.
  • Immunization techniques for mammals may be used to generate anti-Shiga toxin antibodies which are biased away from a selected epitope region(s) of a Shiga toxin A Subunit.
  • polypeptides of the invention may be used in various screening methods, such as, e.g., protein display screening and in vitro selections, for generation, identification, and affinity maturation of various binding domains, such as, e.g., immunoglobulin-type domains, which bind Shiga toxins such that screen selections are biased away from a selected epitope region(s) of a Shiga toxin A Subunit (see G15ckler J et al, Molecules 15: 2478- 90 (2010); Bradbury A et al, Nat Biotechnol 29: 245-54 (2011); Chen T, Keating A, Protein Sci 21 : 949-63 (2012); Geyer C et al, Methods Mol Biol 901 : 1 1-32 (2012)).
  • various binding domains such as, e.g., immunoglobulin-type domains, which bind Shiga toxins such that screen selections are biased away from a selected epitope region(s) of a Shiga toxin A
  • Certain polypeptides of the invention may be used as immunization materials in methods for the creation and/or production of biased anti-Shiga toxin antibodies or anti-toxins. Immunization techniques for mammals may be used to generate anti-Shiga toxin antibodies which are biased away from a selected epitope region(s) of a Shiga toxin A Subunit. For example, certain polypeptides of the invention may be used as an immunization material to generate anti-Shiga toxin A Subunit antibodies which are biased away from a selected epitope region(s) of a Shiga toxin A Subunit.
  • immunization techniques may be used to generate anti-Shiga toxin antibodies biased toward epitopes present on native Shiga toxin B Subunits and/or interfaces between the Shiga toxin subunits present in the holotoxin.
  • anti-Shiga toxin antibodies have uses in methods involving immunodetection assays and for the creation of Shiga toxin neutralizing antibodies or anti-toxins (see Mukherjee J et al, Infect Immun 70: 5896-9 (2002); Sheoran A et al, Infect Immun 71 : 3125-30 (2003); Cheng L et al, Toxins 5: 1845-58 (2013); He X et al., J Immunol Methods 389: 18-28 (2013); Tremblay J et al, Infect Immun 81 : 4592-603 (2013)).
  • certain polypeptides of the invention may be used to better generate Shiga toxin neutralizing antibodies which then may be administered as a protective agent, therapeutic agent, or engineered into a protective and/or therapeutic for the treatment of infections by Shiga toxin producing microorganisms or other exposures to Shiga toxins (see Fujii J et al, Microb Pathog 25: 139-46 (1998); Mukherjee J et al, Infect Immun 70: 5896-9 (2002); Sheoran A et al., Infect Immun 71: 3125-30 (2003); Gao X et al, Vaccine 29: 6656-63 (2011); Cheng L et al, Toxins 5: 1845-58 (2013); He X et al, J Immunol Methods 389: 18-28 (2013); Tremblay J et al, Infect Immun 81: 4592-603 (2013); Vance D et al, J Biol Chem 288: 36538-47 (2013)).
  • Certain polypeptides of the invention may be used as vaccination materials in methods for the creation and/or production of biased anti-Shiga toxin antibodies.
  • Vaccination techniques may be used with compositions comprising certain polypeptides of the invention to confer a mammal with active immunity to a future infection by a Shiga toxin producing microorganism or other exposure to a Shiga toxin (see Bosworth B et al., Infect Immun 64: 55-60 (1996); Rabinovitz B et al., J Dairy Sci 95: 3318-26 (2012)).
  • Vaccine design may take into account the differences between epitopes that elicit neutralizing antibodies versus non-neutralizing antibodies with the possibility of non- neutralizing antibodies interfering with protective, neutralizing antibodies in a subject.
  • the polypeptides of the invention useful as biased immunization and/or vaccination materials may benefit from reductions and/or eliminations of Shiga toxin effector functions, such as enzymatic activity and/or cytotoxicity (He X et al, J Immunol Methods 389: 18-28 (2013); Skinner C et al, PLoS One 9: e99854 (2014)).
  • Reduction or elimination of a Shiga toxin effector function may be accomplished by using one or more truncations and/or amino acid substitutions known to the skilled worker or discovered by the skilled worker using well- known methods.
  • Shiga toxin effector function may be accomplished by using the substitutions described in the Examples which exhibited attenuated, severely reduced, and/or loss of activity in a Shiga toxin effector assay, such as, e.g., ribosome inhibition and targeted cytotoxicity.
  • Such modifications are well known to the skilled worker and include, for example, a methionine added at the amino terminus to provide an initiation site, additional amino acids placed on either terminus to create conveniently located restriction sites or termination codons, and biochemical affinity tags fused to either terminus to provide for convenient detection and/or purification.
  • additional amino acid residues at the amino and/or carboxy termini, such as sequences for epitope tags or other moieties.
  • the additional amino acid residues may be used for various purposes including, e.g., facilitating cloning, facilitating expression, post- translational modification, facilitating synthesis, purification, facilitating detection, and administration.
  • Non-limiting examples of epitope tags and moieties are chitin binding protein domains, enteropeptidase cleavage sites, Factor Xa cleavage sites, FIAsH tags, FLAG tags, green fluorescent proteins (GFP), glutathione-S-transferase moieties, HA tags, maltose binding protein domains, myc tags, polyhistidine tags, ReAsH tags, strep-tags, strep-tag II, TEV protease sites, thioredoxin domans, thrombin cleavage site, and V5 epitope tags.
  • the polypeptide sequence of the de- immunized Shiga toxin effector region polypeptides and/or proteins of the invention are varied by one or more conservative amino acid substitutions introduced into the polypeptide region(s) as long as at least one amino acid is disrupted in at least one natively positioned epitope region provided herein.
  • conservative amino acid substitution denotes that one or more amino acids are replaced by another, biologically similar amino acid residue. Examples include substitution of amino acid residues with similar characteristics, e.g. small amino acids, acidic amino acids, polar amino acids, basic amino acids, hydrophobic amino acids and aromatic amino acids (see, for example, Table B, infra).
  • a conservative substitution with a residue normally not found in endogenous, mammalian peptides and proteins is the conservative substitution of an arginine or lysine residue with, for example, ornithine, canavanine, aminoethylcysteine, or another basic amino acid.
  • conservative substitutions in peptides and proteins see, e.g., Bowie J et al, Science 247: 1306-10 (1990).
  • exemplary conservative substitutions of amino acids are grouped by physicochemical properties - 1: neutral, hydrophilic; II: acids and amides; III: basic; IV: hydrophobic; V: aromatic, bulky amino acids, VI hydrophilic uncharged, VII aliphatic uncharged, VIII non-polar uncharged, IX cycloalkenyl-associated, X hydrophobic, XI polar, XII small, XIII turn-permitting, and XIV flexible.
  • conservative amino acid substitutions include the following: 1) S may be substituted for C; 2) M or L may be substituted for F; 3) Y may be substituted for M; 4) Q or E may be substituted for K; 5) N or Q may be substituted for H; and 6) H may be substituted for N.
  • Additional conservative amino acid substitutions include the following: 1) S may be substituted for C; 2) M or L may be substituted for F; 3) Y may be substituted for M; 4) Q or E may be substituted for K; 5) N or Q may be substituted for H; and 6) H may be substituted for N.
  • the de-immunized Shiga toxin effector region polypeptides and/or proteins of the invention may comprise functional fragments or variants of a polypeptide region of the invention that have, at most, 20, 15, 10, 9, 8, 7, 6, 5, 4, 3, 2, or 1 amino acid substitutions compared to a polypeptide sequence recited herein, as long as it retains a disruption of at least one amino acid in a natively positioned epitope region provided in the Examples (Tables 1, 2, 3, 4, and/or 5) and as long as it exhibits a significant level of a Shiga toxin effector function alone and/or as a component of a therapeutic and/or diagnostic composition.
  • Variants of the de-immunized Shiga toxin effector region polypeptides and/or proteins of the invention are within the scope of the invention as a result of changing a polypeptide of the protein of the invention by altering one or more amino acids or deleting or inserting one or more amino acids, such as within the binding region or the Shiga toxin effector region, in order to achieve desired properties, such as changed cytotoxicity, changed cytostatic effects, changed immunogenicity, and/or changed serum half-life.
  • a de-immunized Shiga toxin effector region polypeptide and/or a polypeptide of a protein of the invention may further be with or without a signal sequence.
  • the de-immunized Shiga toxin effector region polypeptides and/or proteins of the invention shares at least 85%, 90%, 95%, 96%, 97%, 98%, 99% or more amino acid sequence identity to any one of the amino acid sequences of a protein recited herein, as long as it retains a disruption of at least one amino acid in a natively positioned epitope region provided in the Examples (Tables 1, 2, 3, 4, and/or 5) and measurable biological activity, such as cytotoxicity, extracellular target biomolecule binding, enzymatic catalysis, subcellular routing, or catalytically inactivating ribosomes.
  • the de-immunized Shiga toxin effector region polypeptides and/or proteins of the invention may be altered to change the enzymatic activity and/or cytotoxicity of the Shiga toxin effector region as long as at least one amino acid is disrupted in a natively positioned epitope region provided in the Examples (Tables 1, 2, 3, 4, and/or 5). This change may or may not result in a change in the cytotoxicity of the Shiga toxin effector region polypeptide or cytotoxic protein of which the altered Shiga toxin effector region is a component.
  • Possible alterations include mutations to the Shiga toxin effector region polypeptide selected from the group consisting of: a truncation, deletion, inversion, insertion and substitution as long as at least one amino acid is disrupted in a natively positioned epitope region provided in the Examples (Tables 1, 2, 3, 4, and/or 5).
  • the cytotoxicity of the A Subunits of members of the Shiga toxin family may be reduced or eliminated by mutation or truncation.
  • the positions labeled tyrosine-77, glutamate-167, arginine-170, tyrosine- 114, and tryptophan-203 have been shown to be important for the catalytic activity of Stx, Stxl, and Stx2 (Hovde C et al, Proc Natl Acad Sci USA 85: 2568-72 (1988); Deresiewicz R et al, Biochemistry 31 : 3272-80 (1992); Deresiewicz R et al, Mol Gen Genet 241 : 467-73 (1993); Ohmura M et al, Microb Pathog 15: 169-76 (1993); Cao C et al, Microbiol Immunol 38: 441-7 (1994); Suhan M, Hovde C, Infect Immun 66: 5252-9 (1998)). Mutating both glutamate
  • a truncated fragment of Slt-I Al containing residues 1-239 displayed significant enzymatic activity in vitro and cytotoxicity by de novo expression in the cytosol (LaPointe, J Biol Chem 280: 23310-18 (2005)). Expression of a Slt-I Al fragment truncated to residues 1-239 in the endoplasmic reticulum was not cytotoxic because it could not retrotranslocate to the cytosol (LaPointe, J Biol Chem 280: 23310-18 (2005)).
  • Shiga-like toxin 1 A Subunit truncations are catalytically active, capable of enzymatically inactivating ribosomes in vitro, and cytotoxic when expressed within a cell (LaPointe, J Biol Chem 280: 23310-18 (2005)).
  • the smallest Shiga toxin A Subunit fragment exhibiting full enzymatic activity is a polypeptide composed of residues 1-239 of SltlA (LaPointe, J Biol Chem 280: 23310-18 (2005)).
  • substitutions will be known to the skilled worker based on the prior art, such as asparagine at position 75 to alanine, tyrosine at position 77 to serine, substitution of the tyrosine at position 1 14 to serine, substitution of the glutamate at position 167 to glutamate, substitution of the arginine at position 170 to alanine, substitution of the arginine at position 176 to lysine, and/or substitution of the tryptophan at position 203 to alanine.
  • Other mutations which either enhance or reduce Shiga toxin enzymatic activity and/or cytotoxicity are within the scope of the invention and may be determined using well known techniques and assays disclosed herein.
  • the de-immunized Shiga toxin effector region polypeptides and/or proteins of the invention may optionally be conjugated to one or more additional agents which may include therapeutic and/or diagnostic agents known in the art, including such agents as described herein.
  • Shiga toxin effector region polypeptides and proteins of the invention may be produced using biochemical engineering techniques well known to those of skill in the art.
  • Shiga toxin effector region polypeptides and proteins of the invention may be manufactured by standard synthetic methods, by use of recombinant expression systems, or by any other suitable method.
  • Shiga toxin effector region polypeptides and proteins of the invention may be synthesized in a number of ways, including, e.g.
  • methods comprising: (1) synthesizing a polypeptide or polypeptide component of a protein using standard solid-phase or liquid-phase methodology, either stepwise or by fragment assembly, and isolating and purifying the final peptide compound product; (2) expressing a polynucleotide that encodes a polypeptide or polypeptide component of a protein of the invention in a host cell and recovering the expression product from the host cell or host cell culture; or (3) cell-free in vitro expression of a polynucleotide encoding a polypeptide or polypeptide component of a protein of the invention, and recovering the expression product; or by any combination of the methods of (1), (2) or (3) to obtain fragments of the peptide component, subsequently joining (e.g.
  • Shiga toxin effector region polypeptide or a polypeptide or polypeptide component of a protein of the invention may suitably be manufactured by standard synthetic methods.
  • peptides may be synthesized by, e.g. methods comprising synthesizing the peptide by standard solid-phase or liquid-phase methodology, either stepwise or by fragment assembly, and isolating and purifying the final peptide product.
  • De-immunized Shiga toxin effector region polypeptides and proteins of the invention may be prepared (produced and purified) using recombinant techniques well known in the art. In general, methods for preparing
  • polypeptides by culturing host cells transformed or transfected with a vector comprising the encoding polynucleotide and recovering the polypeptide from cell culture are described in, e.g. Sambrook J et al, Molecular Cloning: A Laboratory Manual (Cold Spring Harbor Laboratory Press, NY, U.S., 1989); Dieffenbach C et al, PCR Primer: A Laboratory Manual (Cold Spring Harbor Laboratory Press, N.Y., U.S., 1995). Any suitable host cell may be used to produce a Shiga toxin effector region polypeptide and/or protein of the invention.
  • Host cells may be cells stably or transiently transfected, transformed, transduced or infected with one or more expression vectors which drive expression of a polypeptide of the invention.
  • a Shiga toxin effector region polypeptide and/or protein of the invention may be produced by modifying the polynucleotide encoding a polypeptide or protein of the invention that result in altering one or more amino acids or deleting or inserting one or more amino acids in order to achieve desired properties, such as changed cytotoxicity, changed cytostatic effects, changed immunogenicity, and/or changed serum half-life.
  • host organisms for expression of proteins of the invention include prokaryotes, such as E. coli and B. subtilis, eukaryotic cells, such as yeast and filamentous fungi (like S. cerevisiae, P.
  • yeast pastoris A. awamori, and K. lactis
  • algae like C. reinhardtii
  • insect cell lines mammalian cells (like CHO cells), plant cell lines, and eukaryotic organisms such as transgenic plants (like A. thaliana and N. benthamiana).
  • the present invention also provides methods for producing de-immunized Shiga toxin effector region polypeptides and/or proteins of the invention according to above recited methods and using a polynucleotide encoding part or all of a polypeptide of the invention or a polypeptide component of a protein of the invention, an expression vector comprising at least one polynucleotide of the invention capable of encoding part or all of a polypeptide of the invention when introduced into a host cell, and/or a host cell comprising a polynucleotide or expression vector of the invention.
  • polypeptide or protein When a polypeptide or protein is expressed using recombinant techniques in a host cell or cell-free system, it is advantageous to separate (or purify) the desired polypeptide or protein away from other components, such as host cell factors, in order to obtain preparations that are of high purity or are substantially homogeneous. Purification can be accomplished by methods well known in the art, such as centrifugation techniques, extraction techniques, chromatographic and fractionation techniques (e.g.
  • polypeptides and proteins of the invention may optionally be purified in homo-multimeric forms (i.e. a protein complex of two or more identical polypeptides or proteins of the invention).
  • the present invention provides polypeptides and proteins for use, alone or in combination with one or more additional therapeutic agents, in a pharmaceutical composition, for treatment or prophylaxis of conditions, diseases, disorders, or symptoms described in further detail below (e.g. cancers, malignant tumors, non-malignant tumors, growth abnormalities, immune disorders, and microbial infections).
  • the present invention further provides pharmaceutical compositions comprising a polypeptide or protein of the invention, or a pharmaceutically acceptable salt or solvate thereof, according to the invention, together with at least one pharmaceutically acceptable carrier, excipient, or vehicle.
  • the pharmaceutical composition of the invention may comprise homo-multimeric and/or hetero-multimeric forms of the polypeptides or proteins of the invention.
  • compositions will be useful in methods of treating, ameliorating, or preventing a disease, condition, disorder, or symptom described in further detail below. Each such disease, condition, disorder, or symptom is envisioned to be a separate embodiment with respect to uses of a pharmaceutical composition according to the invention.
  • the invention further provides pharmaceutical compositions for use in at least one method of treatment according to the invention, as described in more detail below.
  • mammals such as the non- limiting examples of primates, livestock animals (e.g. cattle, horses, pigs, sheep, goats, etc.), companion animals (e.g. cats, dogs, etc.) and laboratory animals (e.g. mice, rabbits, rats, etc.).
  • livestock animals e.g. cattle, horses, pigs, sheep, goats, etc.
  • companion animals e.g. cats, dogs, etc.
  • laboratory animals e.g. mice, rabbits, rats, etc.
  • beneficial or desired clinical results include, but are not limited to, reduction or alleviation of symptoms, diminishment of extent of disease, stabilization (e.g. not worsening) of state of disease, delay or slowing of disease progression, amelioration or palliation of the disease state, and remission (whether partial or total), whether detectable or undetectable.
  • Treating can also mean prolonging survival relative to expected survival time if not receiving treatment.
  • a subject e.g. a human
  • the terms “treat,” “treating,” or “treatment” includes inhibition or reduction of an increase in severity of a pathological state or symptoms relative to the absence of treatment, and is not necessarily meant to imply complete cessation of the relevant disease, disorder, or condition.
  • treatment includes reduction in overall tumor burden and/or individual tumor size.
  • prevention may refer to prophylactic or preventive measures.
  • beneficial or desired clinical results include, but are not limited to, prevention or slowing of symptoms, progression or development of a disease, whether detectable or undetectable.
  • a subject e.g. a human
  • prevention includes slowing the onset of disease relative to the absence of treatment, and is not necessarily meant to imply permanent prevention of the relevant disease, disorder or condition.
  • preventing or “prevention” of a condition may in certain contexts refer to reducing the risk of developing the condition, or preventing or delaying the development of symptoms associated with the condition.
  • an "effective amount” or “therapeutically effective amount” is an amount or dose of a composition (e.g. a therapeutic composition or agent) that produces at least one desired therapeutic effect in a subject, such as preventing or treating a target condition or beneficially alleviating a symptom associated with the condition.
  • a composition e.g. a therapeutic composition or agent
  • the most desirable therapeutically effective amount is an amount that will produce a desired efficacy of a particular treatment selected by one of skill in the art for a given subject in need thereof.
  • This amount will vary depending upon a variety of factors understood by the skilled worker, including but not limited to the characteristics of the therapeutic compound (including activity, pharmacokinetics, pharmacodynamics, and bioavailability), the physiological condition of the subject (including age, sex, disease type, disease stage, general physical condition, responsiveness to a given dosage, and type of medication), the nature of the pharmaceutically acceptable carrier or carriers in the formulation, and the route of administration.
  • One skilled in the clinical and pharmacological arts will be able to determine a therapeutically effective amount through routine experimentation, namely by monitoring a subject's response to administration of a compound and adjusting the dosage accordingly (see e.g. Remington: The Science and Practice of Pharmacy (Gennaro A, ed., Mack Publishing Co., Easton, PA, U.S., 19th ed., 1995)).
  • Diagnostic compositions comprise a polypeptide or protein of the invention and one or more detection promoting agents.
  • detection promoting agents are known in the art, such as isotopes, dyes, colorimetric agents, contrast enhancing agents, fluorescent agents, bioluminescent agents, and magnetic agents. These agents may be incorporated into the polypeptide or protein of the invention at any position.
  • the incorporation of the agent may be via an amino acid residue(s) of the cytotoxic protein or via some type of linkage known in the art, including via linkers and/or chelators.
  • the incorporation of the agent is in such a way to enable the detection of the presence of the diagnostic composition in a screen, assay, diagnostic procedure, and/or imaging technique.
  • a protein of the invention may be directly or indirectly linked to one or more detection promoting agents.
  • detection promoting agents known to the skilled worker which can be operably linked to the polypeptides or proteins of the invention for information gathering methods, such as for diagnostic and/or prognostic applications to diseases, disorders, or conditions of an organism (see e.g.
  • detection promoting agents include image enhancing contrast agents, such as fluorescent dyes (e.g.
  • Detection promoting agents may be incorporated directly or indirectly by using an intermediary functional group, such as chelators like 2-benzyl DTPA, PAMAM, NOTA, DOTA, TETA, analogs thereof, and functional equivalents of any of the foregoing (see Leyton J et al, Clin Cancer Res 14: 7488-96 (2008)).
  • an intermediary functional group such as chelators like 2-benzyl DTPA, PAMAM, NOTA, DOTA, TETA, analogs thereof, and functional equivalents of any of the foregoing (see Leyton J et al, Clin Cancer Res 14: 7488-96 (2008)).
  • CT scanning computed tomography imaging
  • optical imaging including direct, fluorescent, and bioluminescent imaging
  • magnetic resonance imaging MRI
  • PET positron emission tomography
  • SPECT single-photon emission computed tomography
  • ultrasound and x-ray computed tomography imaging
  • solvate in the context of the present invention refers to a complex of defined stoichiometry formed between a solute (in casu, a polypeptide compound or pharmaceutically acceptable salt thereof according to the invention) and a solvent.
  • the solvent in this connection may, for example, be water, ethanol or another pharmaceutically acceptable, typically small-molecular organic species, such as, but not limited to, acetic acid or lactic acid.
  • a solvate is normally referred to as a hydrate.
  • Polypeptides and proteins of the present invention, or salts thereof, may be formulated as pharmaceutical compositions prepared for storage or administration, which typically comprise a therapeutically effective amount of a compound of the invention, or a salt thereof, in a pharmaceutically acceptable carrier.
  • pharmaceutically acceptable carrier includes any of the standard pharmaceutical carriers. Pharmaceutically acceptable carriers for therapeutic use are well known in the pharmaceutical art, and are described, for example, in Remington 's Pharmaceutical Sciences (Mack Publishing Co. (A. Gennaro, ed., 1985). As used herein, "pharmaceutically acceptable carrier” includes any and all physiologically acceptable, i.e.
  • Pharmaceutically acceptable carriers or diluents include those used in formulations suitable for oral, rectal, nasal or parenteral (including subcutaneous, intramuscular, intravenous, intradermal, and transdermal) administration.
  • Exemplary pharmaceutically acceptable carriers include sterile aqueous solutions or dispersions and sterile powders for the extemporaneous preparation of sterile injectable solutions or dispersions.
  • aqueous and nonaqueous carriers examples include water, ethanol, polyols (such as glycerol, propylene glycol, polyethylene glycol, and the like), and suitable mixtures thereof, vegetable oils, such as olive oil, and injectable organic esters, such as ethyloleate.
  • polyols such as glycerol, propylene glycol, polyethylene glycol, and the like
  • vegetable oils such as olive oil
  • injectable organic esters such as ethyloleate.
  • the carrier is suitable for intravenous, intramuscular,
  • the cytotoxic protein or other pharmaceutical component may be coated in a material intended to protect the compound from the action of low pH and other natural inactivating conditions to which the active cytotoxic protein may encounter when administered to a patient by a particular route of administration.
  • compositions of the invention may conveniently be presented in unit dosage form and may be prepared by any of the methods well known in the art of pharmacy. In such form, the composition is divided into unit doses containing appropriate quantities of the active component.
  • the unit dosage form can be a packaged preparation, the package containing discrete quantities of the preparations, for example, packeted tablets, capsules, and powders in vials or ampoules.
  • the unit dosage form can also be a capsule, cachet, or tablet itself, or it can be the appropriate number of any of these packaged forms. It may be provided in single dose injectable form, for example in the form of a pen.
  • Compositions may be formulated for any suitable route and means of administration. Subcutaneous or transdermal modes of administration may be particularly suitable for therapeutic proteins described herein.
  • compositions of the invention may also contain adjuvants such as preservatives, wetting agents, emulsifying agents and dispersing agents. Preventing the presence of microorganisms may be ensured both by sterilization procedures, and by the inclusion of various antibacterial and antifungal agents, for example, paraben, chlorobutanol, phenol sorbic acid, and the like. Isotonic agents, such as sugars, sodium chloride, and the like into the compositions, may also be desirable. In addition, prolonged absorption of the injectable pharmaceutical form may be brought about by the inclusion of agents which delay absorption such as, aluminum monostearate and gelatin.
  • adjuvants such as preservatives, wetting agents, emulsifying agents and dispersing agents. Preventing the presence of microorganisms may be ensured both by sterilization procedures, and by the inclusion of various antibacterial and antifungal agents, for example, paraben, chlorobutanol, phenol sorbic acid, and the like. Isot
  • a pharmaceutical composition of the invention also optionally includes a pharmaceutically acceptable antioxidant.
  • exemplary pharmaceutically acceptable antioxidants are water soluble antioxidants such as ascorbic acid, cysteine hydrochloride, sodium bisulfate, sodium metabisulfite, sodium sulfite and the like; oil-soluble antioxidants, such as ascorbyl palmitate, butylated hydroxyanisole (BHA), butylated hydroxytoluene (BHT), lecithin, propylgallate, alpha-tocopherol, and the like; and metal chelating agents, such as citric acid, ethylenediamine tetraacetic acid (EDTA), sorbitol, tartaric acid, phosphoric acid, and the like.
  • water soluble antioxidants such as ascorbic acid, cysteine hydrochloride, sodium bisulfate, sodium metabisulfite, sodium sulfite and the like
  • oil-soluble antioxidants such as ascorbyl palmitate, butylated hydroxyanisole (B
  • the present invention provides pharmaceutical compositions comprising one or a combination of different polypeptides and/or proteins of the invention, or an ester, salt or amide of any of the foregoing, and at least one pharmaceutically acceptable carrier.
  • compositions are typically sterile and stable under the conditions of manufacture and storage.
  • the composition may be formulated as a solution, microemulsion, liposome, or other ordered structure suitable to high drug concentration.
  • the carrier may be a solvent or dispersion medium containing, for example, water, alcohol such as ethanol, polyol (e.g. glycerol, propylene glycol, and liquid polyethylene glycol), or any suitable mixtures.
  • the proper fluidity may be maintained, for example, by the use of a coating such as lecithin, by the maintenance of the required particle size in the case of dispersion and by use of surfactants according to formulation chemistry well known in the art.
  • isotonic agents e.g.
  • compositions sugars, polyalcohols such as mannitol, sorbitol, or sodium chloride may be desirable in the composition.
  • Prolonged absorption of injectable compositions may be brought about by including in the composition an agent that delays absorption for example, monostearate salts and gelatin.
  • Solutions or suspensions used for intradermal or subcutaneous application typically include one or more of: a sterile diluent such as water for injection, saline solution, fixed oils, polyethylene glycols, glycerine, propylene glycol or other synthetic solvents; antibacterial agents such as benzyl alcohol or methyl parabens; antioxidants such as ascorbic acid or sodium bisulfite;
  • a sterile diluent such as water for injection, saline solution, fixed oils, polyethylene glycols, glycerine, propylene glycol or other synthetic solvents
  • antibacterial agents such as benzyl alcohol or methyl parabens
  • antioxidants such as ascorbic acid or sodium bisulfite
  • chelating agents such as ethylenediaminetetraacetic acid
  • buffers such as acetates, citrates or phosphates
  • tonicity adjusting agents such as, e.g., sodium chloride or dextrose.
  • the pH can be adjusted with acids or bases, such as hydrochloric acid or sodium hydroxide, or buffers with citrate, phosphate, acetate and the like.
  • Such preparations may be enclosed in ampoules, disposable syringes or multiple dose vials made of glass or plastic.
  • Sterile injectable solutions may be prepared by incorporating a polypeptide or protein of the invention in the required amount in an appropriate solvent with one or a combination of ingredients described above, as required, followed by sterilization microfiltration.
  • Dispersions may be prepared by incorporating the active compound into a sterile vehicle that contains a dispersion medium and other ingredients, such as those described above.
  • the methods of preparation are vacuum drying and freeze-drying (lyophilization) that yield a powder of the active ingredient in addition to any additional desired ingredient from a sterile-filtered solution thereof.
  • the binding agent When a therapeutically effective amount of a polypeptide or protein of the invention is designed to be administered by, e.g. intravenous, cutaneous or subcutaneous injection, the binding agent will be in the form of a pyrogen-free, parenterally acceptable aqueous solution. Methods for preparing parenterally acceptable protein solutions, taking into consideration appropriate pH, isotonicity, stability, and the like, are within the skill in the art.
  • a preferred pharmaceutical composition for intravenous, cutaneous, or subcutaneous injection will contain, in addition to binding agents, an isotonic vehicle such as sodium chloride injection, Ringer's injection, dextrose injection, dextrose and sodium chloride injection, lactated Ringer's injection, or other vehicle as known in the art.
  • a pharmaceutical composition of the present invention may also contain stabilizers, preservatives, buffers, antioxidants, or other additives well known to those of skill in the art.
  • a polypeptide or protein of the invention may be prepared with carriers that will protect the compound against rapid release, such as a controlled release formulation, including implants, transdermal patches, and microencapsulated delivery systems.
  • a controlled release formulation including implants, transdermal patches, and microencapsulated delivery systems.
  • Biodegradable, biocompatible polymers can be used, such as ethylene vinyl acetate, polyanhydrides, polyglycolic acid, collagen, polyorthoesters, and polylactic acid. Many methods for the preparation of such formulations are patented or generally known to those skilled in the art (see e.g. Sustained and Controlled Release Drug Delivery Systems (Robinson J, ed., Marcel Dekker, Inc., NY, U.S., 1978)).
  • the pharmaceutical composition of the invention may be formulated to ensure a desired distribution in vivo.
  • the blood-brain barrier excludes many large and/or hydrophilic compounds.
  • they can be formulated, for example, in liposomes which may comprise one or more moieties that are selectively transported into specific cells or organs, thus enhancing targeted drug delivery.
  • exemplary targeting moieties include folate or biotin; mannosides; antibodies; surfactant protein A receptor; pl20 catenin and the like.
  • compositions include parenteral formulations designed to be used as implants or particulate systems.
  • implants are depot formulations composed of polymeric or hydrophobic components such as emulsions, ion exchange resins, and soluble salt solutions.
  • particulate systems are microspheres, microparticles, nanocapsules, nanospheres, and nanoparticles (see e.g. Honda M et al, Int J Nanomedicine 8: 495-503 (2013); Sharma A et al, Biomed Res Int 2013 : 960821 (2013); Ramishetti S, Huang L, Ther Deliv 3 : 1429-45 (2012)).
  • Controlled release formulations may be prepared using polymers sensitive to ions, such as, e.g. liposomes, polaxamer 407, and hydroxyapatite.
  • polynucleotide is equivalent to the term “nucleic acids” both of which include polymers of deoxyribonucleic acids (DNAs), polymers of ribonucleic acids (RNAs), analogs of these DNAs or RNAs generated using nucleotide analogs, and derivatives, fragments and homologs thereof.
  • the polynucleotide of the invention may be single-, double-, or triple-stranded.
  • Disclosed polynucleotides are specifically disclosed to include all polynucleotides capable of encoding an exemplary cytotoxic protein, for example, taking into account the wobble known to be tolerated in the third position of RNA codons, yet encoding for the same amino acid as a different RNA codon (see Stothard P,
  • the invention provides polynucleotides which encode a de- immunized Shiga toxin effector region polypeptide and/or a protein of the invention, or a fragment or derivative thereof.
  • the polynucleotides may include, e.g., nucleic acid sequence encoding a polypeptide at least 50%, 55% , 60% , 65%, 70%, 75%, 80%, 85%, 90%, 95%, 99% or more, identical to a polypeptide comprising one of the amino acid sequences of the protein.
  • the invention also includes polynucleotides comprising nucleotide sequences that hybridize under stringent conditions to a polynucleotide which encodes de-immunized Shiga toxin effector region polypeptide and/or a protein of the invention, or a fragment or derivative thereof, or the antisense or complement of any such sequence.
  • Derivatives or analogs of the polynucleotides (or de-immunized Shiga toxin effector region polypeptides and/or proteins) of the invention include, inter alia, polynucleotide (or polypeptide) molecules having regions that are substantially homologous to the polynucleotides, de-immunized Shiga toxin effector region polypeptides, or proteins of the invention, e.g.
  • An exemplary program is the GAP program (Wisconsin Sequence Analysis Package, Version 8 for UNIX,
  • the present invention further provides expression vectors that comprise the polynucleotides within the scope of the invention.
  • the polynucleotides capable of encoding the de-immunized Shiga toxin effector region polypeptides and/or proteins of the invention may be inserted into known vectors, including bacterial plasmids, viral vectors and phage vectors, using material and methods well known in the art to produce expression vectors.
  • Such expression vectors will include the polynucleotides necessary to support production of contemplated Shiga toxin effector region polypeptides and/or proteins of the invention within any host cell of choice or cell-free expression systems (e.g. pTxbl and pIVEX2.3 described in the Examples below).
  • the specific polynucleotides comprising expression vectors for use with specific types of host cells or cell- free expression systems are well known to one of ordinary skill in the art, can be determined using routine experimentation, or may be purchased.
  • expression vector refers to a polynucleotide, linear or circular, comprising one or more expression units.
  • expression unit denotes a polynucleotide segment encoding a polypeptide of interest and capable of providing expression of the nucleic acid segment in a host cell.
  • An expression unit typically comprises a transcription promoter, an open reading frame encoding the polypeptide of interest, and a transcription terminator, all in operable configuration.
  • An expression vector contains one or more expression units.
  • an expression vector encoding a Shiga toxin effector region polypeptide and/or a protein comprising a single polypeptide chain (e.g.
  • a scFv genetically recombined with a Shiga toxin effector region includes at least an expression unit for the single polypeptide chain
  • a protein comprising, e.g. two or more polypeptide chains e.g. one chain comprising a VL domain and a second chain comprising a VH domain linked to a toxin effector region
  • an expression unit for each polypeptide chain may also be separately contained on different expression vectors (e.g. expression may be achieved with a single host cell into which expression vectors for each polypeptide chain has been introduced).
  • Expression vectors capable of directing transient or stable expression of polypeptides and proteins are well known in the art.
  • the expression vectors generally include, but are not limited to, one or more of the following: a heterologous signal sequence or peptide, an origin of replication, one or more marker genes, an enhancer element, a promoter, and a transcription termination sequence, each of which is well known in the art.
  • Optional regulatory control sequences, integration sequences, and useful markers that can be employed are known in the art.
  • host cell refers to a cell which can support the replication or expression of the expression vector.
  • Host cells may be prokaryotic cells, such as E. coli or eukaryotic cells (e.g. yeast, insect, amphibian, bird, or mammalian cells). Creation and isolation of host cell lines comprising a polynucleotide of the invention or capable of producing a polypeptide and/or protein of the invention can be accomplished using standard techniques known in the art.
  • De-immunized Shiga toxin effector region polypeptides and/or proteins within the scope of the present invention may be variants or derivatives of the polypeptides and proteins described herein that are produced by modifying the polynucleotide encoding a polypeptide and/or protein by altering one or more amino acids or deleting or inserting one or more amino acids that may render it more suitable to achieve desired properties, such as more optimal expression by a host cell.
  • the invention relates to a device comprising one or more compositions of matter of the invention, such as a pharmaceutical composition, for delivery to a subject.
  • a delivery device comprising one or more compounds of the invention can be used to administer to a patient a composition of matter of the invention by various delivery methods, including: intravenous, subcutaneous, intramuscular or intraperitoneal injection; oral administration; transdermal administration; pulmonary or transmucosal administration; administration by implant, osmotic pump, cartridge or micro pump; or by other means recognized by a person of skill in the art.
  • kits comprising at least one composition of matter of the invention, and optionally, packaging and instructions for use.
  • Kits may be useful for drug administration and/or diagnostic information gathering.
  • a kit of the invention may optionally comprise at least one additional reagent (e.g., standards, markers and the like). Kits typically include a label indicating the intended use of the contents of the kit.
  • the kit may further comprise reagents and other tools for detecting a cell type (e.g. tumor cell) in a sample or in a subject, or for diagnosing whether a patient belongs to a group that responds to a therapeutic strategy which makes use of a compound, composition or related method of the invention as described herein.
  • a cell type e.g. tumor cell
  • the present invention provides methods of using the polypeptides, proteins, and pharmaceutical compositions of the invention for the targeted killing of cells, for delivering additional exogenous materials into targeted cells, for labeling of the interiors of targeted cells, for collecting diagnostic information, and for treating diseases, disorders, and conditions as described herein.
  • the present invention provides methods of using polypeptides and proteins with specified polypeptide sequences and pharmaceutical compositions thereof.
  • any of the polypeptide sequences in SEQ ID NOs: 4-59 may be specifically utilized as a component of the protein used in the following methods.
  • the present invention provides methods of killing a cell comprising the step of contacting the cell, either in vitro or in vivo, with a polypeptide, protein, or pharmaceutical composition of the present invention.
  • the polypeptides, proteins, and pharmaceutical compositions of the invention can be used to kill a specific cell type upon contacting a cell or cells with one of the claimed compositions of matter.
  • a cytotoxic polypeptide, protein, or pharmaceutical composition of the present invention can be used to kill specific cell types in a mixture of different cell types, such as mixtures comprising cancer cells, infected cells, and/or hematological cells.
  • a cytotoxic polypeptide, protein, or pharmaceutical composition of the present invention can be used to kill cancer cells in a mixture of different cell types.
  • a cytotoxic polypeptide, protein, or pharmaceutical composition of the present invention can be used to kill specific cell types in a mixture of different cell types, such as pre-transplantation tissues.
  • a polypeptide, protein, or pharmaceutical composition of the present invention can be used to kill specific cell types in a mixture of cell types, such as pre-administration tissue material for therapeutic purposes.
  • a polypeptide, protein, or pharmaceutical composition of the present invention can be used to selectively kill cells infected by viruses or microorganisms, or otherwise selectively kill cells expressing a particular extracellular target biomolecule, such as a cell surface biomolecule.
  • the polypeptides, proteins, and pharmaceutical compositions of the invention have varied applications, including, e.g., uses in depleting unwanted cell types from tissues either in vitro or in vivo, uses in modulating immune responses to treat graft versus host disease, uses as antiviral agents, uses as anti-parasitic agents, and uses in purging transplantation tissues of unwanted cell types.
  • cytotoxic polypeptide In certain embodiments, a cytotoxic polypeptide, protein, or
  • composition of the present invention can show potent cell-kill activity when administered to a population of cells, in vitro or in vivo in a subject such as in a patient in need of treatment.
  • this potent cell-kill activity can be restricted to specifically and selectively kill certain cell types within an organism, such as certain cancer cells, neoplastic cells, malignant cells, non-malignant tumor cells, or infected cells.
  • the present invention provides a method of killing a cell in a patient in need thereof, the method comprising the step of administering to the patient at least one cytotoxic polypeptide or protein of the present invention, or a pharmaceutical composition thereof.
  • cytotoxic polypeptide, protein, or pharmaceutical compositions thereof can be used to kill a cancer cell in a patient by targeting an extracellular biomolecule found physically coupled with a cancer or tumor cell.
  • cancer cell or “cancerous cell” refers to various neoplastic cells which grow and divide in an abnormally accelerated fashion and will be clear to the skilled person.
  • tumor cell includes both malignant and non-malignant cells.
  • cancers and/or tumors can be defined as diseases, disorders, or conditions that are amenable to treatment and/or prevention.
  • the cancers and tumors (either malignant or non-malignant) which are comprised by cancer cells and/or tumor cells will be clear to the skilled person.
  • Neoplastic cells are often associated with one or more of the following: unregulated growth, lack of differentiation, local tissue invasion, angiogenesis, and metastasis.
  • Certain embodiments of the cytotoxic polypeptide or protein of the invention, or pharmaceutical compositions thereof, can be used to kill an immune cell (whether healthy or malignant) in a patient by targeting an extracellular biomolecule found physically coupled with an immune cell.
  • cytotoxic polypeptide or protein of the invention can be used to kill an infected cell in a patient by targeting an extracellular biomolecule found physically coupled with an infected cell.
  • the protein of the invention can be used in a method for prophylaxis of organ and/or tissue transplant rejection wherein the donor organ or tissue is perfused prior to transplant with a cytotoxic protein of the invention or a pharmaceutical composition thereof in order to purge the organ of donor T-cells and/or B-cells (see e.g. Alpdogan O, van den Brink M, Semin Oncol 39: 629-42 (2012)).
  • cytotoxic polypeptide or protein of the invention can be used to kill an infected cell in a patient by targeting an extracellular biomolecule found physically coupled with an infected cell.
  • the present invention provides a method of treating a disease, disorder, or condition in a patient comprising the step of administering to a patient in need thereof a therapeutically effective amount of at least one of the cytotoxic polypeptide or protein of the invention, or a pharmaceutical composition thereof.
  • Contemplated diseases, disorders, and conditions that can be treated using this method include cancers, malignant tumors, non-malignant tumors, growth abnormalities, immune disorders, and microbial infections.
  • Administration of a "therapeutically effective dosage" of a compound of the invention can result in a decrease in severity of disease symptoms, an increase in frequency and duration of disease symptom-free periods, or a prevention of impairment or disability due to the disease affliction.
  • the therapeutically effective amount of a compound of the present invention will depend on the route of administration, the type of mammal being treated, and the physical characteristics of the specific patient under
  • This amount and the method of administration can be tailored to achieve optimal efficacy, and may depend on such factors as weight, diet, concurrent medication and other factors, well known to those skilled in the medical arts.
  • the dosage sizes and dosing regimen most appropriate for human use may be guided by the results obtained by the present invention, and may be confirmed in properly designed clinical trials.
  • An effective dosage and treatment protocol may be determined by conventional means, starting with a low dose in laboratory animals and then increasing the dosage while monitoring the effects, and systematically varying the dosage regimen as well. Numerous factors may be taken into consideration by a clinician when determining an optimal dosage for a given subject. Such considerations are known to the skilled person.
  • An acceptable route of administration may refer to any administration pathway known in the art, including but not limited to aerosol, enteral, nasal, ophthalmic, oral, parenteral, rectal, vaginal, or transdermal (e.g. topical administration of a cream, gel or ointment, or by means of a transdermal patch).
  • "Parenteral administration” is typically associated with injection at or in communication with the intended site of action, including infraorbital, infusion, intraarterial, intracapsular, intracardiac, intradermal, intramuscular,
  • the dosage range will generally be from about 0.0001 to 100 milligrams per kilogram (mg/kg), and more, usually 0.01 to 5 mg/kg, of the host body weight.
  • Exemplary dosages may be 0.25 mg/kg body weight, 1 mg/kg body weight, 3 mg/kg body weight, 5 mg/kg body weight or 10 mg/kg body weight or within the range of 1-10 mg/kg.
  • An exemplary treatment regime is a once or twice daily administration, or a once or twice weekly administration, once every two weeks, once every three weeks, once every four weeks, once a month, once every two or three months or once every three to 6 months. Dosages may be selected and readjusted by the skilled health care professional as required to maximize therapeutic benefit for a particular patient.
  • compositions of the invention will typically be administered to the same patient on multiple occasions. Intervals between single dosages can be, for example, 2-5 days, weekly, monthly, every two or three months, every six months, or yearly. Intervals between administrations can also be irregular, based on regulating blood levels or other markers in the subject or patient. Dosage regimens for a compound of the invention include intravenous administration of 1 mg/kg body weight or 3 mg/kg body weight with the compound administered every two to four weeks for six dosages, then every three months at 3 mg/kg body weight or 1 mg/kg body weight.
  • a pharmaceutical composition of the present invention may be administered via one or more routes of administration, using one or more of a variety of methods known in the art. As will be appreciated by the skilled worker, the route and/or mode of administration will vary depending upon the desired results. Routes of administration for polypeptides, proteins, and pharmaceutical compositions of the invention include, e.g. intravenous, intramuscular, intradermal, intraperitoneal, subcutaneous, spinal, or other parenteral routes of administration, for example by injection or infusion.
  • a polypeptide, protein, or pharmaceutical composition of the invention may be administered by a non-parenteral route, such as a topical, epidermal or mucosal route of administration, for example, intranasally, orally, vaginally, rectally, sublingually, or topically.
  • a non-parenteral route such as a topical, epidermal or mucosal route of administration, for example, intranasally, orally, vaginally, rectally, sublingually, or topically.
  • Therapeutic polypeptides, proteins, or pharmaceutical compositions of the invention may be administered with one or more of a variety of medical devices known in the art.
  • a pharmaceutical composition of the invention may be administered with a needleless hypodermic injection device.
  • implants and modules useful in the present invention are in the art, including e.g., implantable micro-infusion pumps for controlled rate delivery; devices for administering through the skin; infusion pumps for delivery at a precise infusion rate; variable flow implantable infusion devices for continuous drug delivery; and osmotic drug delivery systems. These and other such implants, delivery systems, and modules are known to those skilled in the art.
  • a polypeptide, protein, or pharmaceutical composition of the present invention may be administered alone or in combination with one or more other therapeutic or diagnostic agents.
  • a combination therapy may include a cytotoxic protein of the invention or pharmaceutical composition thereof combined with at least one other therapeutic agent selected based on the particular patient, disease or condition to be treated.
  • agents include, inter alia, a cytotoxic, anti-cancer or chemotherapeutic agent, an anti-inflammatory or antiproliferative agent, an antimicrobial or antiviral agent, growth factors, cytokines, an analgesic, a therapeutically active small molecule or polypeptide, a single chain antibody, a classical antibody or fragment thereof, or a nucleic acid molecule which modulates one or more signaling pathways, and similar modulating therapeutics which may complement or otherwise be beneficial in a therapeutic or prophylactic treatment regimen.
  • Treatment of a patient with a polypeptide, protein, or pharmaceutical composition of the invention preferably leads to cell death of targeted cells and/or the inhibition of growth of targeted cells.
  • cytotoxic proteins of the invention, and pharmaceutical compositions comprising them will be useful in methods for treating a variety of pathological disorders in which killing or depleting target cells may be beneficial, such as, inter alia, cancer, tumors, other growth abnormalities, immune disorders, and infected cells.
  • the present invention provides methods for suppressing cell proliferation, and treating cell disorders, including neoplasia, overactive B-cells, and overactive T-cells.
  • polypeptides, proteins, and pharmaceutical compositions of the invention can be used to treat or prevent cancers, tumors (malignant and non-malignant), growth abnormalities, immune disorders, and microbial infections.
  • the above ex vivo method can be combined with the above in vivo method to provide methods of treating or preventing rejection in bone marrow transplant recipients, and for achieving immunological tolerance.
  • the present invention provides methods for treating malignancies or neoplasms and other blood cell associated cancers in a mammalian subject, such as a human, the method comprising the step of administering to a subject in need thereof a therapeutically effective amount of a cytotoxic protein or pharmaceutical composition of the invention.
  • the cytotoxic polypeptides, proteins, and pharmaceutical compositions of the invention have varied applications, including, e.g., uses in removing unwanted T-cells, uses in modulating immune responses to treat graft-versus- host disease, uses as antiviral agents, uses as antimicrobial agents, and uses in purging transplantation tissues of unwanted cell types.
  • the cytotoxic polypeptides, proteins, and pharmaceutical compositions of the present invention are commonly anti-neoplastic agents - meaning they are capable of treating and/or preventing the development, maturation, or spread of neoplastic or malignant cells by inhibiting the growth and/or causing the death of cancer or tumor cells.
  • a polypeptide, protein, or pharmaceutical composition of the present invention is used to treat a B-cell-, plasma cell- or antibody- mediated disease or disorder, such as for example leukemia, lymphoma, myeloma, Human Immunodeficiency Virus-related diseases, amyloidosis, hemolytic uremic syndrome, polyarteritis, septic shock, Crohn's Disease, rheumatoid arthritis, ankylosing spondylitis, psoriatic arthritis, ulcerative colitis, psoriasis, asthma, Sjorgren's syndrome, graft-versus-host disease, graft rejection, diabetes, vasculitis, scleroderma, and systemic lupus erythematosus.
  • a B-cell-, plasma cell- or antibody- mediated disease or disorder such as for example leukemia, lymphoma, myeloma, Human Immunodeficiency Virus-related diseases, amyloidosis,
  • certain embodiments of the polypeptides, proteins, and pharmaceutical compositions of the present invention are antimicrobial agents - meaning they are capable of treating and/or preventing the acquisition, development, or consequences of microbiological pathogenic infections, such as caused by viruses, bacteria, fungi, prions, or protozoans.
  • T-cells or B-cells it is within the scope of the present invention to provide a prophylaxis or treatment for diseases or conditions mediated by T-cells or B-cells by administering the cytotoxic protein or the invention, or a pharmaceutical composition thereof, to a patient for the purpose of killing T-cells or B-cells in the patient.
  • This usage is compatible with preparing or conditioning a patient for bone marrow transplantation, stem cell transplantation, tissue transplantation, or organ transplantation, regardless of the source of the transplanted material, e.g. human or non-human sources.
  • the cytotoxic polypeptides, proteins, and pharmaceutical compositions of the present invention can be utilized in a method of treating cancer comprising administering to a patient, in need thereof, a therapeutically effective amount of a cytotoxic polypeptide, protein, or pharmaceutical composition of the present invention.
  • the cancer being treated is selected from the group consisting of: bone cancer (such as multiple myeloma or Ewing's sarcoma), breast cancer, central/peripheral nervous system cancer (such as brain cancer, neurofibromatosis, or
  • glioblastoma a malignant neoplasm originating from a mammal.
  • gastrointestinal cancer such as stomach cancer or colorectal cancer
  • germ cell cancer such as ovarian cancers and testicular cancers
  • glandular cancer such as pancreatic cancer, parathyroid cancer
  • pheochromocytoma salivary gland cancer, or thyroid cancer
  • head-neck cancer such as nasopharyngeal cancer, oral cancer, or pharyngeal cancer
  • hematological cancers such as leukemia, lymphoma, or myeloma
  • kidney- urinary tract cancer such as renal cancer and bladder cancer
  • liver cancer lung/pleura cancer (such as mesothelioma, small cell lung carcinoma, or non- small cell lung carcinoma)
  • prostate cancer sarcoma (such as angiosarcoma, fibrosarcoma, Kaposi's sarcoma, or synovial sarcoma), skin cancer (such as basal cell carcinoma, squamous cell carcinoma, or melanoma), and uterine cancer.
  • sarcoma such as angiosarcoma, fibrosarcoma, Kaposi's sarcoma, or synovial sarcoma
  • skin cancer such as basal cell carcinoma, s
  • polypeptides, proteins, and pharmaceutical compositions of the present invention can be utilized in a method of treating an immune disorder comprising administering to a patient, in need thereof, a therapeutically effective amount of the cytotoxic protein or a pharmaceutical composition of the present invention.
  • the immune disorder is related to an inflammation associated with a disease selected from the group consisting of: amyloidosis, ankylosing spondylitis, asthma, Crohn's disease, diabetes, graft rejection, graft-versus-host disease, Hashimoto's thyroiditis, hemolytic uremic syndrome, HIV-related diseases, lupus erythematosus, multiple sclerosis, polyarteritis, psoriasis, psoriatic arthritis, rheumatoid arthritis, scleroderma, septic shock, Sjorgren's syndrome, ulcerative colitis, and vasculitis.
  • a disease selected from the group consisting of: amyloidosis, ankylosing spondylitis, asthma, Crohn's disease, diabetes, graft rejection, graft-versus-host disease, Hashimoto's thyroiditis, hemolytic uremic syndrome, HIV-related diseases, lupus erythematosus, multiple sclerosis, poly
  • polypeptide or protein of the invention is using the polypeptide or protein of the invention as a component of a pharmaceutical composition or medicament for the treatment or prevention of a cancer, tumor, other growth abnormality, immune disorder, and/or microbial infection.
  • immune disorders presenting on the skin of a patient may be treated with such a medicament in efforts to reduce inflammation.
  • skin tumors may be treated with such a medicament in efforts to reduce tumor size or eliminate the tumor completely.
  • cytotoxic polypeptides, proteins, and pharmaceutical compositions of the invention may be used in molecular neurosurgery applications such as immunolesioning and neuronal tracing (see, Wiley R, Lappi D, Adv Drug Deliv Rev 55: 1043-54 (2003), for review).
  • the targeting domain may be selected or derived from various ligands, such as neurotransmitters and neuropeptides, which target specific neuronal cell types by binding neuronal surface receptors, such as a neuronal circuit specific G-protein coupled receptor.
  • the targeting domain may be selected from or derived from antibodies that bind neuronal surface receptors. Because Shiga toxins robustly direct their own retrograde axonal transport, certain cytotoxic proteins of the invention may be used to kill a neuron(s) which expresses the extracellular target at a site of cytotoxic protein injection distant from the cell body (see Llewellyn-Smith I et al, JNeurosci Methods 103: 83-90 (2000)).
  • neuronal cell-type-specific -targeting cytotoxic polypeptides and proteins have uses in neuroscience research, such as for elucidating mechanisms of sensations (see e.g. Mishra S, Hoon M, Science 340: 968-71 (2013)), and creating model systems of neurodegenerative diseases, such as Parkinson's and Alzheimer's (see e.g. Hamlin A et al, PLoS One e53472 (2013)).
  • a method of using a polypeptide, protein, pharmaceutical composition, and/or diagnostic composition of the invention to label or detect the interiors of neoplastic cells and/or immune cell types is a method of using a polypeptide, protein, pharmaceutical composition, and/or diagnostic composition of the invention to label or detect the interiors of neoplastic cells and/or immune cell types. Based on the ability of certain polypeptides, proteins, and pharmaceutical compositions of the invention to enter specific cell types and route within cells via retrograde intracellular transport, the interior compartments of specific cell types are labeled for detection. This can be performed on cells in situ within a patient or on cells and tissues removed from an organism, e.g. biopsy material.
  • a method of using a polypeptide, protein, pharmaceutical composition, and/or diagnostic composition of the invention to detect the presence of a cell type for the purpose of information gathering regarding diseases, conditions and/or disorders comprises contacting a cell with a diagnostically sufficient amount of a cytotoxic molecule to detect the cytotoxic molecule by an assay or diagnostic technique.
  • diagnostically sufficient amount refers to an amount that provides adequate detection and accurate measurement for information gathering purposes by the particular assay or diagnostic technique utilized.
  • the diagnostically sufficient amount for whole organism in vivo diagnostic use will be a non-cumulative dose of between 0.1 mg to 100 mg of the detection promoting agent linked protein of the invention per kg of subject per subject.
  • the amount of polypeptide or protein of the invention used in these information gathering methods will be as low as possible provided that it is still a diagnostically sufficient amount.
  • the amount of polypeptide, protein, or pharmaceutical composition of the invention administered to a subject will be as low as feasibly possible.
  • the cell-type specific targeting of polypeptides and proteins of the invention combined with detection promoting agents provides a way to detect and image cells physically coupled with an extracellular target biomolecule of a binding region of the molecule of the invention.
  • Imaging of cells using the polypeptides or proteins of the invention may be performed in vitro or in vivo by any suitable technique known in the art. Diagnostic information may be collected using various methods known in the art, including whole body imaging of an organism or using ex vivo samples taken from an organism.
  • sample used herein refers to any number of things, but not limited to, fluids such as blood, urine, serum, lymph, saliva, anal secretions, vaginal secretions, and semen, and tissues obtained by biopsy procedures.
  • various detection promoting agents may be utilized for non-invasive in vivo tumor imaging by techniques such as magnetic resonance imaging (MRI), optical methods (such as direct, fluorescent, and bioluminescent imaging), positron emission tomography (PET), single-photon emission computed tomography (SPECT), ultrasound, x-ray computed tomography, and combinations of the aforementioned (see, Kaur S et al, Cancer Lett 315: 97-1 11 (2012), for review).
  • MRI magnetic resonance imaging
  • optical methods such as direct, fluorescent, and bioluminescent imaging
  • PET positron emission tomography
  • SPECT single-photon emission computed tomography
  • ultrasound x-ray computed tomography
  • a polypeptide, protein, or pharmaceutical composition of the invention is a method of using a polypeptide, protein, or pharmaceutical composition of the invention as a diagnostic composition to label or detect the interiors of cancer, tumor, and/or immune cell types (see e.g., Koyama Y et al, Clin Cancer Res 13 : 2936-45 (2007); Ogawa M et al, Cancer Res 69: 1268-72 (2009); Yang L et al, Small 5: 235-43 (2009)).
  • the interior compartments of specific cell types are labeled for detection. This can be performed on cells in situ within a patient or on cells and tissues removed from an organism, e.g. biopsy material.
  • Diagnostic compositions of the invention may be used to characterize a disease, disorder, or condition as potentially treatable by a related
  • compositions of matter of the invention may be used to determine whether a patient belongs to a group that responds to a therapeutic strategy which makes use of a compound, composition or related method of the invention as described herein or is well suited for using a delivery device of the invention.
  • Diagnostic compositions of the invention may be used after a disease, e.g. a cancer, is detected in order to better characterize it, such as to monitor distant metastases, heterogeneity, and stage of cancer progression.
  • a disease e.g. a cancer
  • the phenotypic assessment of disease disorder or infection can help prognostication and prediction during therapeutic decision making.
  • certain methods of the invention may be used to discriminate localized versus systemic problems.
  • Diagnostic compositions of the invention may be used to assess responses to therapeutic(s) regardless of the type of therapeutic, e.g. small molecule drug, biological drug, or cell-based therapy.
  • certain embodiments of the diagnostics of the invention may be used to measure changes in tumor size, changes in antigen positive cell populations including number and distribution, or monitoring a different marker than the antigen targeted by a therapy already being administered to a patient (see Smith- Jones P et al, Nat. Biotechnol 22: 701-6 (2004); Evans M et al, Proc. Natl. Acad. Sci. U.S.A. 108: 9578-82 (201 1)).
  • Certain embodiments of the method used to detect the presence of a cell type may be used to gather information regarding diseases, disorders, and conditions, such as, for example bone cancer (such as multiple myeloma or Ewing's sarcoma), breast cancer, central/peripheral nervous system cancer (such as brain cancer, neurofibromatosis, or glioblastoma), gastrointestinal cancer (such as stomach cancer or colorectal cancer), germ cell cancer (such as ovarian cancers and testicular cancers, glandular cancer (such as pancreatic cancer, parathyroid cancer, pheochromocytoma, salivary gland cancer, or thyroid cancer), head-neck cancer (such as nasopharyngeal cancer, oral cancer, or pharyngeal cancer), hematological cancers (such as leukemia, lymphoma, or myeloma), kidney -urinary tract cancer (such as renal cancer and bladder cancer), liver cancer, lung/pleura cancer (such as mesothelioma
  • lymphoproliferative disorders multiple sclerosis, myasthenia gravis, neuroinflammation, polyarteritis, psoriasis, psoriatic arthritis, rheumatoid arthritis, scleroderma, septic shock, Sjorgren's syndrome, systemic lupus erythematosus, ulcerative colitis, vasculitis, cell proliferation, inflammation, leukocyte activation, leukocyte adhesion, leukocyte chemotaxis, leukocyte maturation, leukocyte migration, neuronal differentiation, acute lymphoblastic leukemia (ALL), T acute lymphocytic leukemia/lymphoma (ALL), acute myelogenous leukemia, acute myeloid leukemia (AML), B-cell chronic lymphocytic leukemia (B-CLL), B-cell prolymphocytic lymphoma, Burkitt's lymphoma (BL), chronic lymphocytic leukemia (CLL), chronic myelogen
  • polypeptides and proteins of the invention are used for both diagnosis and treatment, or for diagnosis alone.
  • polypeptides of the invention have uses as immunization materials for eliciting immune responses to specific epitopes based on the presence of a disruption(s) in a selected epitope region(s).
  • a polypeptide of the invention may be used as an immunization material for the administration to a mammal and/or used in a display screen to generate an immunoglobulin domain recognizing a Shiga toxin.
  • the present invention is further illustrated by the following non-limiting examples of selectively cytotoxic proteins comprising de-immunized Shiga toxin effector regions derived from A Subunits of members of the Shiga toxin family and binding regions capable of binding extracellular target biomolecules physically coupled to specific cell types.
  • de-immunized Shiga toxin effector polypeptides demonstrate the retention of Shiga toxin effector functions as components of various cytotoxic proteins.
  • the exemplary cytotoxic proteins bound to target biomolecules expressed by targeted cell types and entered the targeted cells.
  • the internalized cytotoxic proteins effectively routed their de- immunized Shiga toxin effector regions to the cytosol to inactivate ribosomes and subsequently caused the apoptotic death of the targeted cells similar to cytotoxic proteins comprising wild-type Shiga toxin effector regions.
  • Linear B-cell epitopes were predicted for the mature A Subunit of Shiga- like toxin 1 (SLT-1A; SEQ ID NO: l) from the polypeptide sequence and 3D structural data of Shiga-Like Toxin Chain A (PDB ID: 1DM0 A) by Prolmmune Inc. (Sarasota, FL, U.S.) using their REVEAL® system.
  • SLT-1A Shiga-like toxin 1
  • PDB ID: 1DM0 A 3D structural data of Shiga-Like Toxin Chain A
  • B-cell epitopes were predicted from the amino acid sequences of the A Subunits of Shiga toxin (StxA; SEQ ID NO:2), Shiga-like toxin 1 (SLT- 1A; SEQ ID NO: l), and Shiga-like toxin 2 (Stx2A; SEQ ID NO:3) using the BcePred webserver (Saha S, Raghava G, Lecture Notes in Comput Sci 3239: 197-204 (2004)), Bepipred Linear Epitope Prediction (Larsen J et al., Immunome Res 2: 2 (2006)), and ElliPro Antibody epitope prediction (Haste Andersen P et al, Protein Sci 15: 2558-67 (2006); Ponomarenko J, Bourne P, BMC Struct Biol 7: 64 (2007)).
  • the various computational methods revealed similar predictions for B-cell epitope regions in the three prototypical Shiga toxin A Subunits (Tables 1-3).
  • the Immune Epitope Database (IEDB) curated by the National Institutes of Allergy and Infectious Diseases of the U.S. (NIAID) is said to provide all experimentally characterized B- and T-cell epitopes of Shiga toxins.
  • IEDB Immune Epitope Database
  • NIAID National Institutes of Allergy and Infectious Diseases of the U.S.
  • IEDB provides only a single epitope for only a single Shiga toxin A Subunit (Stx2dA): IEDB identification number 1 10493, an experimentally determined, discontinuous B-cell epitope comprising amino acids 42-49, 96-100, and 245- 260 (Smith M et al, Infect Immun 77: 2730-40 (2009)).
  • Shiga toxin A Subunits were analyzed using the Epitopia webserver for predicting B-cell epitopes and immunogenic residues (Rubinstein N et al, BMC Bioinformatics 10: 287 (2009)).
  • Epitopia was used to identify linear amino acid residue regions predicted to be immunogenic in SLT-IA based on an Epitopia score of 4 or 5 ("high") for the majority of amino acid residues in a linear amino acid residue stretch.
  • the Epitopia analysis predicted an immunogenic region occurs from amino acid residues 1 to 15 in SLT-IA (designated as Epitope Region 0 below, see Table 5, infra).
  • the immunogenic epitope region 2 in SLT-IA (see Table 4) might include position 49.
  • the immunogenic epitope region 3 in SLT-IA (see Table 4) might include position 53 and extend to around position 62-66 (designated as Epitope Region 3* below, see Table 5, infra)
  • the Epitope Region 4 in SLT-IA (see Table 4) might include position 94 (designated as Epitope Region 4* below, see Table 5, infra)
  • the epitope region 6 in SLT-IA (see Table 4) might start at position 179 and extend to around position 188-190 (designated as Epitope Region 6* below, see Table 5, infra).
  • Note the starred B-cell epitope regions all completely encompass their respective overlapping region with the same numerical identifier.
  • This assay uses multiple overlapping peptide sequences from the subject protein to test for the elicitation of any immune response by CD4+ T-cells from healthy donor cell samples depleted of CD8+ T-cells.
  • a Shiga toxin effector polypeptide region was derived from the A Subunit of Shiga-like Toxin 1 (SLT-1A).
  • a polynucleotide that encoded amino acids 1-251 of SLT-1A was used as a template to create various polynucleotides encoding various Shiga toxin effector polypeptides with one or more disruptions of a predicted B-cell epitope(s).
  • Shiga toxin effector polypeptides comprising one or more epitope disruptions were expressed from these polynucleotides to explore which disruptions might most effectively de- immunize various Shiga toxin effector polypeptides in the context of a cytotoxic protein of the invention.
  • epitope region #0 the threonine natively located at position 4 in the mature A Subunits of Shiga-like toxin 1 (SEQ ID NO: 1) and and Shiga toxin (SEQ ID NO:2) was mutated to isoleucine (T4I).
  • epitope region #0 the serine natively located at position 8 in the mature A Subunits of Shiga-like toxin 1 (SEQ ID NO: 1) and and Shiga toxin (SEQ ID NO:2) was mutated to isoleucine (S8I).
  • epitope region #0 the threonine natively located at position 9 in the mature A Subunits of Shiga-like toxin 1 (SEQ ID NO: 1) and and Shiga toxin (SEQ ID NO:2) was mutated to isoleucine (T9I) and to valine (T9V).
  • the lysine natively located at position 1 1 in the mature A Subunits of Shiga-like toxin 1 (SEQ ID NO: 1) and and Shiga toxin (SEQ ID NO:2) was mutated to alanine (Kl 1A) and to histidine (Kl 1H).
  • Kl, T4, S8, T9, and Kl 1 were predicted by the Epitopia webserver to be solvent exposed.
  • epitope region #2 In epitope region #2 (see Table 5), the serine natively located at position 45 in the mature A Subunit of Shiga-like toxin 1 (SEQ ID NO: 1) was mutated to valine (S45V) and to isoleucine (S45I). In epitope region #2 (see Table 5), the aspartate natively located at position 47 in the mature A Subunit of Shiga-like toxin 1 (SEQ ID NO: 1) was mutated to glycine (D47G).
  • the D53 residue was predicted by the Epitopia webserver to be solvent exposed and have an immunogenicity scale value of 5 or "high.”
  • epitope region #3 and #3* see Table 5
  • epitope region #3 and #3* the aspartate natively located at position 58 in the mature A Subunit of Shiga-like toxin 1 (SEQ ID NO: 1) and Shiga toxin (SEQ ID NO:2) was mutated to alanine (D58A), to valine (D58V), and to phenylalanine (D58F).
  • the proline natively located at position 59 in the mature A Subunit of Shiga-like toxin 1 (SEQ ID NO: 1) and Shiga toxin (SEQ ID NO:2) was mutated to alanine (P59A).
  • epitope region #3 and #3* the glutamate natively located at position 60 in the mature A Subunit of Shiga-like toxin 1 (SEQ ID NO: 1) and Shiga toxin (SEQ ID NO:2) was mutated to isoleucine (E60I), to threonine (E60T), and to arginine (E60R).
  • the glutamate natively located at position 61 in the mature A Subunit of Shiga-like toxin 1 (SEQ ID NO: 1) and Shiga toxin (SEQ ID NO:2) was mutated to alanine (E61A), to valine (E61V), and to leucine (E61L).
  • epitope region #4* (see Table 5), the aspartate natively located at position 94 in the mature A Subunit of Shiga-like toxin 1 (SEQ ID NO: 1) and Shiga toxin (SEQ ID NO:2) was mutated to alanine (D94A). This D94 residue was predicted by the Epitopia webserver to be solvent exposed and have an immunogenicity scale value of 5 or "high.”
  • epitope region #4 and #4* see Table 5
  • epitope region #4 and #4* see Table 5
  • the serine natively located at position 109 in the mature A Subunit of Shiga-like toxin 1 (SEQ ID NO: 1) and Shiga toxin (SEQ ID NO:2) was mutated to valine (S109V).
  • the glycine natively located at position 110 in the mature A Subunit of Shiga-like toxin 1 (SEQ ID NO: l) and Shiga toxin (SEQ ID NO:2) was mutated to alanine (Gl 10A).
  • epitope region #4 and #4* see Table 5
  • the serine natively located at position 1 12 in the mature A Subunit of Shiga-like toxin 1 (SEQ ID NO: 1) and Shiga toxin (SEQ ID NO:2) was mutated to valine (S I 12V).
  • Shiga-like toxin 1 (SEQ ID NO: l) and Shiga toxin (SEQ ID NO:2) was mutated to glycine (T180G).
  • T180G glycine
  • epitope region #6 and #6* see Table 5
  • epitope region #6 and #6* see Table 5
  • the aspartate natively located at position 183 in the mature A Subunit of Shiga-like toxin 1 (SEQ ID NO: 1) and Shiga toxin (SEQ ID NO:2) was mutated to alanine (D183A) and to glycine (D183G).
  • the aspartate natively located at position 184 in the mature A Subunit of Shiga-like toxin 1 (SEQ ID NO: 1) and Shiga toxin (SEQ ID NO:2) was mutated to alanine (D184A) or phenylalanine (D184F).
  • epitope region #6 and #6* see Table 5
  • the leucine natively located at position 185 in the mature A Subunit of Shiga-like toxin 1 (SEQ ID NO: 1) and Shiga toxin (SEQ ID NO:2) was mutated to valine (LI 85V).
  • the serine natively located at position 186 in the mature A Subunit of Shiga-like toxin 1 (SEQ ID NO: 1) and Shiga toxin (SEQ ID NO:2) was mutated to alanine (S 186A) and to phenylalanine (S 186F).
  • epitope region #6 and #6* the glycine natively located at position 187 in the mature A Subunit of Shiga-like toxin 1 (SEQ ID NO: 1) and Shiga toxin (SEQ ID NO:2) was mutated to alanine (G187A).
  • the arginine natively located at position 188 in the mature A Subunit of Shiga-like toxin 1 (SEQ ID NO: 1) and Shiga toxin (SEQ ID NO:2) was mutated to alanine (R188A) and to leucine (R188L).
  • Shiga-like toxin 1 (SEQ ID NO: l) and Shiga toxin (SEQ ID NO:2) was mutated to alanine (R251A).
  • the amino acid substitution comprising Shiga toxin effector polypeptides were tested as components of putative cytotoxic proteins with cell-targeting binding regions.
  • the cytotoxic proteins comprised an immunoglobulin-type binding region and Shiga toxin effector region linked together to form a fusion protein.
  • These putative cytotoxic fusion proteins were produced by expression from polynucleotides encoding them using a bacterial system known in the art.
  • the ribosome inactivation capabilities of de-immunized cytotoxic proteins were determined using a cell-free, in vitro protein translation assay using the TNT® Quick Coupled Transcription/Translation kit (LI 170 Promega Madison, WI, U.S.).
  • the kit includes Luciferase T7 Control DNA (L4821 Promega Madison, WI, U.S.) and TNT® Quick Master Mix.
  • the ribosome activity reaction was prepared according to manufacturer's instructions.
  • a series of 10-fold dilutions of the protein comprising a mutated Shiga toxin effector polypeptide region to be tested was prepared in an appropriate buffer and a series of identical TNT reaction mixture components were created for each dilution.
  • Each sample in the dilution series was combined with each of the TNT reaction mixtures along with the Luciferase T7 Control DNA.
  • the test samples were incubated for 1.5 hours at 30 degrees Celsius (°C). After the incubation, Luciferase Assay Reagent (E1483 Promega, Madison, WI, U.S.) was added to all test samples and the amount of luciferase protein translation was measured by luminescence according to manufacturer's instructions. The level of translational inhibition was determined by non-linear regression analysis of log- transformed concentrations of total protein versus relative luminescence units.
  • ICso half maximal inhibitory concentration
  • Exemplary Shiga toxin effector polypeptide regions which exhibited ribosome inhibition are indicated in Table 7. As reported in Table 7, a substitution-comprising construct exhibiting an ICso within 10-fold of a wild- type SLT-1A control construct is considered to exhibit ribosome inhibition activity comparable to wild-type; a construct exhibiting an ICso between 10-fold to 100-fold of a wild-type SLT-1A control is considered to exhibit attenuated activity as compared to wild-type; and a construct exhibiting an IC50 greater than
  • Target-expressing cells were plated (2 x 10 3 cells per well for adherent cells, plated the day prior to protein addition or 7.5 x 10 3 cells per well for suspension cells, plated the same day as protein addition) in 20 ⁇ , cell culture medium in 384 well plates.
  • a series of 10-fold dilutions of each protein comprising a mutated Shiga toxin effector polypeptide region to be tested was prepared in an appropriate buffer, and 5 ⁇ , of the dilutions or buffer control were added to the cells. Control wells containing only media were used for baseline correction.
  • the cell samples were incubated with the proteins or just buffer for 3 days at 37°C and in an atmosphere of 5% carbon dioxide (CO2). The total cell survival or percent viability was determined using a luminescent readout using the CellTiter-Glo® Luminescent Cell Viability Assay (G7573 Promega Madison, WI, U.S.) according to the manufacturer's instructions.
  • the Percent Viability of experimental wells was calculated using the following equation: (Test RLU - Average Media RLU) / (Average Cells RLU - Average Media RLU) * 100.
  • Log polypeptide concentration versus Percent Viability was plotted in Prism (GraphPad Prism, San Diego, CA, U.S.) and log (inhibitor) versus response (3 parameter) analysis was used to determine the half-maximal cytotoxic concentration (CD50) value for the tested proteins.
  • the CD50 for each protein comprising a de-immunized Shiga toxin effector polypeptide and wild-type control protein with no internal epitope disruptions were calculated.
  • cytotoxicity of exemplary Shiga toxin effector polypeptide regions is indicated in Table 8.
  • Table 8 a substitution-comprising construct exhibiting a CD50 within 10-fold of a wild-type SLT-1A control construct is considered to exhibit cytotoxicity comparable to a wild-type; a construct exhibiting a CD50 between 10-fold to 100-fold of a wild-type SLT-1A control is considered to exhibit attenuated cytotoxicity as compared to wild-type; and a construct exhibiting a CD50 greater than 100-fold of a wild-type SLT-1 A control is considered severely impaired/inactive.
  • Table 8 Cytotoxic Activities of Exemplary Shiga Toxin Effector
  • uccessful is used to mean one or more amino acid residue substitutions in a predicted epitope region resulted in a Shiga toxin effector region polypeptide which retained one or more Shiga toxin effector functions.
  • both epitope regions #0 and #4 & 4* successfully tolerated multiple amino acid substitutions within their respective regions (Tables 7 and 8: K1M/K1 1A and D94A/S96I). Reinforcing the idea that various exemplary substitutions in the same epitope region may be combined to create epitope disruptions with greater overall epitope disruption while still retaining significant levels of one or more Shiga toxin effector function.
  • Shiga toxin effector region polypeptides were tested for Shiga toxin effector functions and epitope disruption using the methods as described in the Examples herein, where the Shiga toxin effector region polypeptides comprised multiple amino acids substitutions within a single predicted B-cell epitope region.
  • the regions tested were the following natively positioned regions present in the mature A Subunit of Shiga-like toxin 1 (SEQ ID NO: l) and Shiga toxin (SEQ ID NO:2): 4-12, 43-52, 53-61, 104-1 12, and 180-188.
  • constructs comprised one or more of the following amino acid substitutions in various combinations with other amino acid substitutions in a single region: region 4-12: T4I, T9V, and K11H; region 43-52: S45V, D47G, N48V, N48F, and L49A; region 53-61 : D53G, D53N, R55V, R55L, D58V, E60T, E61V and E61L; region 104-112: S109V, Gl 10A, and SI 12V; region 180-188: T180G, T181I, D183G, L185V, S186F, and R188L.
  • Western analysis of these constructs showed reduced or abolished recognition of each construct by one or more antibodies that can recognize wild-type SLT-IA (mAbl, pAbl, and pAb2 described in Example 4).
  • epitope region #7 is disrupted by the substitution R248A or R251 without any significant effect on either ribosome inhibition activity or cytotoxicity.
  • R248A or R251A may be successfully introduced into the exemplary Shiga toxin effector region polypeptides described above without altering either ribosome inhibition or cytotoxicity.
  • Cytotoxic proteins comprising Streptag® II and wildtype Shiga toxin effector polypeptide regions or de-immunized Shiga toxin effector polypeptide regions were loaded in equal amounts to replicate 4-20% sodium dodecyl sulfate (SDS) polyacrylamide gels (Lonza, Basel, CH) and electrophoresed under denaturing conditions. The resulting gels were either analyzed by Coomassie staining or transferred to polyvinyl difluoride (PVDF) membranes using the iBlot® (Life Technologies, Carlsbad, CA, U.S.) system according to manufacturer's instructions.
  • SDS sodium dodecyl sulfate
  • PVDF polyvinyl difluoride
  • the resulting membranes were probed under standard conditions using the following antibodies: rabbit polyclonal a- NWSHPQFEK (A00626, Genscript, Piscataway, NJ, U.S.) which recognizes the polypeptide NWSHPQFEK also known as Streptag® II, mouse monoclonal a- StxA (anti-SLT- ⁇ mAbl or mAbl) (BEI R-867 BEI Resources, Manassas, VA, U.S.), rabbit polyclonal antibody a-SLT-lA (anti-SLT- ⁇ pAbl or pAbl) (Harlan Laboratories, Inc.
  • RGIDPEEGRFNN spans the putative B-cell epitope region #3 (Table 5), and the peptide sequence
  • HGQDSVRVGR is located at 214-223 in SLT-1A and StxA.
  • Membrane bound antibodies were detected using standard conditions and, when appropriate, using horseradish peroxidase (HRP) conjugated secondary antibodies (goat anti-rabbit- HRP or goat anti-mouse-HRP, Thermo Scientific, Rockford, IL, U.S.).
  • HRP horseradish peroxidase
  • Figures 2-5 show Western blots with the lanes of the gels and/or membranes numbered and the figure legends indicate by the same respective numbering which Shiga toxin effector regions were comprised within the protein loaded into each lane.
  • the S45I/G1 10A/G147A and S33I/G110A/G147A triple substitution mutants showed partial disruption of at least one of the epitopes recognized by a-SLT-lA pAbl ( Figure 3).
  • the S45I/G1 10A/G147A triple mutant strongly disrupted the epitope recognized by the monoclonal antibody mAbl and partially disrupted the epitope recognized by the polyclonal a-SLT-lA pAb2 ( Figure 3; Figure 4).
  • the D58A/G1 10A/G147A triple mutant very effectively disrupted the epitope recognized by the monoclonal antibody mAb 1 and at least one of the epitopes recognized by the polyclonal a-SLT-lA pAb2 ( Figure 3; Figure 4).
  • the D 183 A/D 184A/R188A triple mutant showed very effective disruption of the epitope recognized by the monoclonal antibody mAb 1 ( Figure 5).
  • the D58A/G1 10/G147A/R188A quadruple mutant very effectively disrupted the epitope recognized by the monoclonal antibody mAbl and at least one of the epitopes recognized by the polyclonal a-SLT-lA pAb2 and partially disrupted at least one of the epitopes recognized by a-SLT-lA pAbl ( Figure 5).
  • the epitopes disrupted in the D58A/G110A/G147A triple, S45I/G1 10A/G147A triple, and D58A/G110A/G147A/R188A quadruple mutants (one recognized by mAbl and others recognized by pAb2) most likely reside in two non-continuous regions.
  • the D58A/G1 10A/G147A triple, S45I/G1 10A/G147A triple, and D58A/G110A/G147A/R188A quadruple substitution mutants each comprised a de-immunized Shiga toxin effector region polypeptide verified empirically to have at least two different epitopes disrupted simultaneously.
  • S33I/S45I/D58A/G1 10A/G147A quintuple mutants most likely reside in at least two non-continuous regions.
  • S33I/G1 10A/G147A triple, D58A/G110A/G147A/R188A quadruple, and S33I/S45I/D58A/G1 10A/G147A quintuple mutants probably comprised a de- immunized Shiga toxin effector region polypeptide verified empirically to have at least two different epitopes disrupted simultaneously.
  • a standard ELISA was used to measure the ability of mAbl to recognize a de-immunized Shiga toxin effector region with multiple epitope regions disrupted in the context of a cytotoxic protein.
  • the cytotoxic protein bound the target biomolecule of its scFv binding region.
  • the wells of Nunc MaxiSorp® plates in phosphate buffered saline (IX PBS) (Hyclone Brand, Fisher Scientific, Waltham, MA, U.S.) were coated with recombinant human target protein of the binding region of the cytotoxic protein. The plates were incubated overnight at 4°C.
  • cytotoxic protein comprising a Streptag® II and a de-immunized Shiga toxin effector region (D58A/G1 10A/G147A/R188A) was added to the wells at a concentration determined to be above the binding dissociation constant (KD).
  • KD binding dissociation constant
  • the plates were incubated at room temperature for one hour to allow for cytotoxic protein binding under non-denaturing conditions.
  • the wells were washed with PBS-T and then incubated with either PBS-T or the mouse monoclonal antibody anti-SLT-lA mAbl for one hour at room temperature.
  • the wells were washed in PBS-T and then incubated with the detection antibodies: HRP-conjugated antibody directed to Streptag® II or an anti-mouse-HRP- conjugated antibody.
  • the wells were washed in PBS-T and then incubated with Pierce TMB Ultra (Thermo Scientific Inc., Rockford, IL, U.S.). The reactions were stopped with 250 mM hydrochloric acid (HC1).
  • Products of HRP activity were detected by a plate reading device measuring absorbance (Abs) of light set to the wavelength of 450 nanometers (nm).
  • the measured absorbance values were corrected for background by subtracting the absorbance values for coated, blocked wells incubated with PBS instead of any Shiga toxin construct.
  • Example 4 Each substitution made in Example 4 with an aim to de-immunize a Shiga toxin effector polypeptide while retaining Shiga toxin effector functions was checked for abolishment of the predicted B-cell epitope in the epitope region comprising the substitution using the BcePred webserver with the following: flexibility readout with the default settings of hydrophilicity 2, accessibility 2, exposed surface 2.4, antigenic propensity 1.8, flexibility 1.9, turns 1.9, polarity 2.3, and combined 1.9 (Saha S, Raghava G, Lecture Notes in Comput Sci 3239: 197-204 (2004)). Table 10 shows the substitution present in the analysis and the result of the B-cell epitope prediction in the last column.
  • epitope regions #0 (1-15) and #7 (243-257) were not predicted in wild-type SLT-1A by the BcePred flexibility approach with the default settings.
  • the substitutions tested did not create de novo any predicted B-cell epitopes by the BcePred flexibility approach (see e.g. Table 10), including KIM, S8I, T9I, Kl 1A in epitope region #0; D94A in epitope region #4*; and S96I in epitope regions #4 and 4*.
  • the results for other substitutions analyzed using the BcePred computational approach are listed in Table 10 that were not yet empirically tested.
  • Example 6 Empirically Testing the Relative Immunogenicity of a De- Immunized Shiga Toxin Effector Polypeptide Compared to a Wild-Type Shiga Toxin Effector Polypeptide Using a Mammalian Model
  • the relative immunogenicity of a de-immunized cytotoxic protein of the invention compared to a non-de-immunized cytotoxic protein was determined using a mammalian model of the human immune system.
  • a murine model of mammalian immune systems was used to compare the relative immunogenicity of an exemplary cytotoxic protein comprising an exemplary de-immunized Shiga toxin effector polypeptide to the parental cytotoxic protein comprising a Shiga toxin effector region with only wild-type sequences.
  • bacterium-derived Shiga toxin effector region polypeptides are foreign (or non-self) molecular structures to mammals, it was expected that the wild-type Shiga toxin effector polypeptide would exhibit some level of immunogenicity.
  • the relative immunogenicity of a non-mammalian protein determined using mice are generally indicative of its relative immunogenicity for all mammals.
  • cytotoxic proteins comprising either a wild-type Shiga toxin effector polypeptide (amino acids 1-251 of SLT-1A) or an exemplary de-immunized Shiga toxin effector region polypeptide (amino acids 1-251 of SLT-1A with certain amino acid substitutions).
  • Female BALB/c mice were randomly assigned to groups to form groups with six mice each. First, serum samples were collected from each mouse prior to exposure to a cytotoxic protein.
  • each mouse in a group was administered 0.25 mg/kg per dose of the cytotoxic protein comprising either a wild-type (amino acids 1-251 of SLT-1A) or an exemplary de-immunized Shiga toxin effector region (amino acids 1-251 of SLT-1A comprising D58A/G1 10A/G147A/R188A) by intra-peritoneal injection three times a week over a duration of two weeks for a total of six injections over twelve days.
  • murine sera were collected from mice from all the groups to observe anti- "administered protein" levels using an in-solution ELISA assay.
  • the in-solution anti-"cytotoxic protein" ELISA assay was performed as follows. The same cytotoxic protein used for injections in a mouse group was incubated overnight at 4°C in solution with the serum of mice from that group, and then the immune complex (consisting of the cytotoxic protein bound to any induced antibodies in the serum) was captured using ELISA plate wells coated with the appropriate target protein. Captured immune complexes comprising murine IgGs were detected using a horseradish-peroxidase-conjugated, anti- mouse IgG, secondary antibody.
  • ELISA plates were developed to detect horsereadish peroxidase activity, and the horsereadish peroxidase activity or "ELISA signal” was measured at 450 nm using a plate reader.
  • the "ELISA signal” or “ELISA values” were calculated as the absorbance values after subtracting the background signal as measured with a "no serum” negative control. For this in-solution ELISA assay and setup, greater ELISA values indicate stronger immune responses (antibody induction).
  • mice in any group were measured by this in-solution ELISA assay to have pre-formed serum antibodies recognizing either cytotoxic protein prior to exposure to a cytotoxic protein via injection.
  • any post- administration detection of anti-"cytotoxic protein" antibodies in these mice using the in-solution ELISA assay represents induced de novo antibody formation which occurred after administration.
  • the same cytotoxic protein injected into a group of mice was used in the ELISA assay to capture serum antibodies from the mice of that group.
  • the antibodies present in the sera from mice in the "wild-type Shiga toxin effector region” group were captured in the ELISA assay with the cytotoxic protein comprising a wild-type Shiga toxin effector region
  • the antibodies present in sera from the mice in the "de-immunized Shiga toxin effector region polypeptide” group were captured in the ELISA assay with the exemplary cytotoxic protein comprising the exemplary de-immunized Shiga toxin effector region polypeptide (D58A/G1 10A/G147A/R188A).
  • mice in the group administered the cytotoxic protein comprising a wild- type Shiga toxin effector region had a higher magnitude of antibody response as shown by the ELISA signal than the mice in the group administered the cytotoxic protein comprising the de-immunized Shiga toxin effector region (D58A/G1 10A/G147A/R188A) at both Day 15 and 22 ( Figure 7).
  • the mean ELISA signal (quantitating antibody response) for the "de-immunized Shiga toxin effector region polypeptide" group was 25% (Day 15) and 39% (Day 22) of the "wild-type Shiga toxin effector region" group.
  • the ELISA signal differences between the "de-immunized Shiga toxin effector region polypeptide" and the "wild-type Shiga toxin effector region” groups were statistically significant based on t-tests (p value was less than 0.005). Using a nominal absorbance value cutoff of 0.9 Abs units to represent a "strong" antibody response, 6/6 (100%) mice in the "wild-type Shiga toxin effector region” group had a strong antibody response at Days 15 or 22, whereas only 3/6 (50%) mice in the "de-immunized Shiga toxin effector region polypeptide” group had a strong antibody response.
  • the exemplary cytotoxic protein comprising the de- immunized Shiga toxin effector region polypeptide (D58A/G1 10A/G147A/R188A) showed reduced immunogenicity in a mammalian model (Figure 7).
  • the decrease in the overall magnitude of antibody induction in mice in the "de-immunized Shiga toxin effector region polypeptide” group, as well as the reduction in the number of mice in this group which induced a potent antibody response, as compared to the "wild-type Shiga toxin effector region” group shows that the de-immunized Shiga toxin effector region polypeptide (D58A/G1 10A/G147A/R188A) was successfully de- immunized (i.e. has reduced immunogenic potential in mammals), and the exemplary cytotoxic protein comprising it is a de-immunized cytotoxic protein (i.e. has reduced immunogenic potential in mammals).
  • This exemplary de-immunized cytotoxic protein comprised a Shiga toxin effector region polypeptide comprising four different B-cell epitope region disruptions while retaining three or more Shiga toxin effector functions:
  • this exemplary cytotoxic protein is a de-immunized cytotoxic protein comprising a de-immunized Shiga toxin effector region polypeptide which has both reduced antigenicity and immunogenicity to mammalian immune systems.
  • the antigenicity and/or immunogenicity of this exemplary cytotoxic protein may be further reduced by introducing additional mutations in the same or additional predicted B-cell epitope regions.
  • mice are intravenously administered either the de- immunized or wildtype forms 4 times at 7 day intervals.
  • Blood samples are taken from the injected mice and tested by ELISA assays for reactivity to the cytotoxic proteins and/or the Shiga toxin effector polypeptide. Relatively reduced immunogenic responses will be measured in mice injected with certain exemplary de-immunized Shiga toxin effector polypeptides or cytotoxic protein comprising the same as compared to molecules comprising Shiga toxin effector region polypeptides comprising only wild-type amino acid sequences.
  • Certain exemplary de-immunized cytotoxic protein comprising exemplary de-immunized Shiga toxin effector region polypeptides comprising multiple B-cell epitope region disruptions will retain at a significant level of one or more Shiga toxin effector function: catalytic ribosome inhibition, intracellular routing, and cytotoxicity and have reduced recognition by pre-formed antibodies recognizing anti-Shiga-like Toxin A Subunit antibodies both western blot and/or an ELISA assay.
  • exemplary cytotoxic protein comprising de-immunized Shiga toxin effector region polypeptides with multiple B-cell epitope region disruptions are de-immunized Shiga toxin effector region polypeptides with reduced antigenicity and/or immunogenicity.
  • substitutions at specific amino acid positions shown herein as successfully tolerating substitutions are most likely to be successful for retaining at least one Shiga toxin effector function when substituted with certain other amino acids.
  • the demonstration that cytotoxic proteins comprising Shiga toxin effector regions retained cytotoxicity when multiple single amino acid substitutions (predicted to disrupt an epitope region and that retained cytotoxicity) were combined suggests that successful single amino acid substitution may generally be combined with other successful amino acid substitutions in a different epitope region to generate de-immunized Shiga toxin effector polypeptides which retain significant Shiga toxin effector function(s).
  • Examples of similar conservative amino acid substitutions include Kl to A, G, V, L, I, F, and H; T4I to A, G, V, L, F, M, and S; S8 to A, G, V, L, F, and M; T9 to A, G, L, F, M, and S; Kl 1 to G, V, L, I, F, and M; S33 to A, G, V, L, F, and M; S45 to A, G, L, F, and M; T45 to A, G, V, L, I, F, and M; D47 to A, V, L, I, F, S, and Q; N48 to A, G, L, I, and M; L49 to G; D53 to V, L, I, F, S, and Q; R55 to G, I, F, M, Q, S, K, and H; D58 to G, V, L, I, S, and Q; P59 to G; E60 to A, G, V, F, S, Q, N,
  • Amino acid substitutions which remove charge, polarity, and/or reduce side chain length will also be able to disrupt an epitope while maintaining at least one Shiga toxin effector function. For example, substituting A, G, V, L, I, P, C, M, F, S, D, N, Q, H, and K for amino acid residue Kl, T4, S8, T9, Kl 1, S33, S45, D47, N48, L49, D53, R55, 157, D58, ⁇ 59, E60, E61, G62, D94, S96, S109, T109, G110, S112, G147, T180, T181, D183, D184, L185, S186, G187, R188, SI 89, R205, R248, or R251 such that side chain charge is removed, polarity is removed, and/or side chain length is reduced.
  • amino acid substitution in one epitope region of a Shiga toxin effector polypeptide which disrupts an epitope while retaining significant Shiga toxin effector function is generally predicted to be combinable with other amino acid substitutions in the same or a different epitope region which disrupts an epitope while retaining significant Shiga toxin effector function to form a de- immunized Shiga toxin effector polypeptide with multiple epitope regions disrupted while still retaining a significant level of a Shiga toxin effector function.
  • KIM, S8I, T9I, S9I, K11A, S33I, S45I, D53A, R55A, D58A, D58F, P59A, E60I, E60R, E61A, G62A, D94A, S96I, G110A, G147A, D183A, D184A, D184F, S186A, G187A, R188A, S 189A, and/or R205A may be combined where possible with KIM, S8I, T9I, S9I, Kl 1A, S33I, S45I, D53A, R55A, D58A, D58F, P59A, E60I, E60R, E61A, G62A, D94A, S96I, Gl 10A, G147A, D183A, D184A, D 184F, S 186A, G187A, R188A, S189A, and/or R205A to create de-immunized Shiga toxin effect
  • Example 7 A Cytotoxic Protein Comprising a De-Immunized Shiga Toxin Effector Polypeptide and a Binding Region Specific to CD20 (aCD20 fused with SLT-1A)
  • the Shiga toxin effector region is a de-immunized Shiga toxin effector polypeptide derived from the A subunit of Shiga-like Toxin 1
  • An immunoglobulin-type binding region aCD20-antigen is derived from an immunoglobulin-type domain recognizing human CD20 (see e.g. Haisma et al, Blood 92: 184-90 (1999); Geng S et al, Cell Mol Immunol 3: 439-43 (2006); Olafesn T et al., Protein Eng Des Sel 23: 243-9 (2010)), which comprises an immunoglobulin-type binding region capable of binding an extracellular part of CD20.
  • CD20 is expressed on multiple cancer cell types, such as, e.g., B-cell lymphoma cells, hairy cell leukemia cells, B-cell chronic lymphocytic leukemia cells, and melanoma cells.
  • B-cell lymphoma cells such as, e.g., B-cell lymphoma cells, hairy cell leukemia cells, B-cell chronic lymphocytic leukemia cells, and melanoma cells.
  • CD20 is an attractive target for therapeutics to treat certain autoimmune diseases, disorders, and conditions involving overactive B-cells.
  • the immunoglobulin-type binding region aCD20 and Shiga toxin effector region are linked together.
  • a fusion protein is produced by expressing a polynucleotide encoding the aCD20-antigen-binding protein SLT-lA::aCD20 ⁇ see, e.g., SEQ ID NOs: 53, 54, 55, and 56).
  • Expression of the SLT-lA::aCD20 cytotoxic protein is accomplished using either bacterial and/or cell-free, protein translation systems as described in the previous examples or known to the skilled worker.
  • the binding characteristics, the maximum specific binding (Bmax) and equilibrium binding constants (KD), of the cytotoxic protein of this example for CD20+ cells and CD20- cells is determined by a fluorescence-based, flow- cytometry assay.
  • the Bmax for SLT-lA::aCD20 to CD20+ cells is measured to be approximately 50,000-200,000 MFI with a KD within the range of 0.01-100 nM, whereas there is no significant binding to CD20- cells in this assay.
  • the ribosome inactivation abilities of the SLT-lA::aCD20 cytotoxic protein is determined in a cell-free, in vitro protein translation as described above in the previous examples.
  • the inhibitory effect of the cytotoxic protein of this example on cell-free protein synthesis is significant.
  • the ICso of SLT- lA::aCD20 on protein synthesis in this cell-free assay is approximately 0.1-100 pM.
  • the cytotoxicity characteristics of SLT-lA::aCD20 are determined by the general cell-kill assay as described above in the previous examples using CD20+ cells.
  • the selective cytotoxicity characteristics of SLT- lA::aCD20 are determined by the same general cell-kill assay using CD20- cells as a comparison to the CD20+ cells.
  • the CD50 of the cytotoxic protein of this example is approximately 0.01-100 nM for CD20+ cells depending on the cell line.
  • the CD50 of the cytotoxic protein is approximately 10-10,000 fold greater (less cytotoxic) for cells not expressing CD20 on a cellular surface as compared to cells which do express CD20 on a cellular surface.
  • SLT- 1 A: :aCD20 The relative de-immunization of SLT- 1 A: :aCD20 is determined in relation to a wild-type Shiga toxin effector region polypeptide using western analyses, ELISA analyses, and murine models as described in Examples 4 and 6.
  • the Shiga toxin effector region was derived from the A subunit of Shiga-like Toxin 1 (SLT-1A) and comprising one or more de- immunizing amino acid substitutions described in the previous examples.
  • the immunoglobulin-type binding region is aHER2 VHH derived from a single- domain variable region of the camelid antibody (VHH) protein 5F7, as described in U.S. Patent Application Publication 201 1/0059090. Construction, Production, and Purification of the Cytotoxic Protein "otHER2- VHH fused with SLT- 1 A"
  • the immunoglobulin-type binding region and Shiga toxin effector region are linked together to form a fused protein (see, e.g., SEQ ID NOs: 57, 58, and 59).
  • a polynucleotide encoding the (XHER2-VHH variable region derived from protein 5F7 may be cloned in frame with a polynucleotide encoding a linker known in the art and in frame with a polynucleotide encoding the Shiga toxin effector region comprising amino acids of SEQ ID NOs:4-52.
  • Variants of "(XHER2-VHH fused with SLT-IA” cytotoxic proteins are created such that the binding region is optionally located adjacent to the amino-terminus of the Shiga toxin effector region and optionally comprises a carboxy -terminal endoplasmic reticulum signal motif of the KDEL family.
  • Expression of the "(XHER2-VHH fused with SLT-IA” cytotoxic protein variants is accomplished using either bacterial and/or cell-free, protein translation systems as described in the previous examples.
  • the binding characteristics of the cytotoxic protein of this example for HER2+ cells and HER2- cells is determined by a fluorescence-based, flow- cytometry assay.
  • the Bmax for "(XHER2-VHH fused with SLT-IA" variants to HER2+ cells is measured to be approximately 50,000-200,000 MFI with a KD within the range of 0.01-100 nM, whereas there is no significant binding to HER2- cells in this assay.
  • the ribosome inactivation abilities of the "(XHER2-VHH fused with SLT- IA" cytotoxic proteins are determined in a cell-free, in vitro protein translation as described above in the previous examples.
  • the inhibitory effect of the cytotoxic protein of this example on cell-free protein synthesis is significant.
  • the IC50 of "(XHER2-VHH fused with SLT-IA" variants on protein synthesis in this cell-free assay is approximately 0.1-100 pM.
  • the cytotoxicity characteristics of "(XHER2-VHH fused with SLT-IA” variants are determined by the general cell-kill assay as described above in the previous examples using HER2+ cells.
  • the selective cytotoxicity characteristics of "(XHER2-VHH fused with SLT-IA” are determined by the same general cell-kill assay using HER2- cells as a comparison to the HER2+ cells.
  • the CD50 of the cytotoxic protein of this example is approximately 0.01-100 nM for HER2+ cells depending on the cell line.
  • the CD50 of the cytotoxic protein is approximately 10-10,000 fold greater (less cytotoxic) for cells not expressing HER2 on a cellular surface as compared to cells which do express HER2 on a cellular surface.
  • cytotoxic protein XHER2-VHH fused with SLT-1 A on neoplastic cells.
  • mice strains are used to test the effect of the cytotoxic protein after intravenous administration on xenograft tumors in mice resulting from the injection into those mice of human neoplastic cells which express HER2 on their cell surfaces.
  • Example 9 A Cytotoxic Protein Comprising a De-Immunized Shiga Toxin Effector Polypeptide and a Binding Region Derived from the Antibody aEpstein-Barr-Antigen
  • the Shiga toxin effector region is a de-immunzied Shiga toxin effector polypeptide derived from the A subunit of Shiga-like Toxin 1 (SLT-1 A) and comprising one or more de-immunizing amino acid substitutions described in the previous examples.
  • An immunoglobulin-type binding region aEpstein-Barr-antigen is derived from a monoclonal antibody against an Epstein Barr antigen (Fang C et al, J Immunol Methods 287: 21-30 (2004)), which comprises an immunoglobulin-type binding region capable of binding a human cell infected by the Epstein-Barr virus or a transformed cell expressing an Epstein-Barr antigen.
  • Epstein-Barr antigen is expressed on multiple cell types, such as cells infected by an Epstein-Barr virus and cancer cells (e.g. lymphoma and naspharnygeal cancer cells). In addition, Epstein-Barr infection is associated with other diseases, e.g., multiple sclerosis. Construction, Production, and Purification of the Cytotoxic Protein SLT- 1 A: :otEpsteinBarr: :KDEL
  • the immunoglobulin-type binding region aEpstein-Barr-antigen and Shiga toxin effector region are linked together, and a carboxy -terminal KDEL is added to form a protein.
  • a fusion protein is produced by expressing a polynucleotide encoding the aEpstein-Barr-antigen-binding protein SLT-lA::aEpsteinBarr::KDEL. Expression of the SLT- lA::aEpsteinBarr::KDEL cytotoxic protein is accomplished using either bacterial and/or cell-free, protein translation systems as described in the previous examples.
  • the binding characteristics of the cytotoxic protein of this example for Epstein-Barr antigen positive cells and Epstein-Barr antigen negative cells is determined by a fluorescence-based, flow-cytometry assay.
  • the Bmax for SLT- lA::aEpsteinBarr::KDEL to Epstein-Barr antigen positive cells is measured to be approximately 50,000-200,000 MFI with a KD within the range of 0.01- 100 nM, whereas there is no significant binding to Epstein-Barr antigen negative cells in this assay.
  • the ribosome inactivation abilities of the SLT-lA::aEpsteinBarr::KDEL cytotoxic protein is determined in a cell-free, in vitro protein translation as described above in the previous examples.
  • the inhibitory effect of the cytotoxic protein of this example on cell-free protein synthesis is significant.
  • the ICso of SLT-lA::aEpsteinBarr::KDEL on protein synthesis in this cell-free assay is approximately 0.1 -100 pM.
  • the cytotoxicity characteristics of SLT-lA: :aEpsteinBarr::KDEL are determined by the general cell-kill assay as described above in the previous examples using Epstein-Barr antigen positive cells.
  • the selective cytotoxicity characteristics of SLT-lA::aEpsteinBarr::KDEL are determined by the same general cell-kill assay using Epstein-Barr antigen negative cells as a
  • the CD50 of the cytotoxic protein of this example is approximately 0.01-100 nM for Epstein-Barr antigen positive cells depending on the cell line.
  • the CD50 of the cytotoxic protein is approximately 10-10,000 fold greater (less cytotoxic) for cells not expressing the Epstein-Barr antigen on a cellular surface as compared to cells which do express the Epstein-Barr antigen on a cellular surface.
  • Example 10 A Cytotoxic Protein Comprising a De-Immunized Shiga Toxin Effector Polypeptide and a Binding Region Derived from the Antibody aLeishmania-Antigen
  • the Shiga toxin effector region is a de-immunized Shiga toxin effector polypeptide derived from the A subunit of Shiga-like Toxin 1 (SLT-1A) and comprising one or more de-immunizing amino acid substitutions described in the previous examples.
  • SLT-1A Shiga-like Toxin 1
  • An immunoglobulin-type binding region aLeishmania-antigen is derived from an antibody generated, using techniques known in the art, to a cell-surface Leishmania antigen present on human cells harboring an intracellular trypanosomatid protozoa (see Silveira T et al, Int J Parasitol 31 : 1451-8 (2001); Kenner J et al, J Cutan Pathol 26: 130-6 (1999); Berman J and Dwyer, Clin Exp Immunol 44: 342-348 (1981)). Construction, Production, and Purification of the Cytotoxic Protein SLT- 1 A : : gLeishmania: : KDEL
  • the immunoglobulin-type binding region a-Leishmania-antigen and Shiga toxin effector region are linked together, and a carboxy -terminal KDEL is added to form a protein.
  • a fusion protein is produced by expressing a polynucleotide encoding the Leishmania-antigen-binding protein SLT-lA::aLeishmania::KDEL. Expression of the SLT- lA::aLeishmania::KDEL cytotoxic protein is accomplished using either bacterial and/or cell-free, protein translation systems as described in the previous examples.
  • the binding characteristics of the cytotoxic protein of this example for Leishmania antigen positive cells and Leishmania antigen negative cells is determined by a fluorescence-based, flow-cytometry.
  • the Bmax for SLT- lA::aLeishmania::KDEL to Leishmania antigen positive cells is measured to be approximately 50,000-200,000 MFI with a KD within the range of 0.01 - 100 nM, whereas there is no significant binding to Leishmania antigen negative cells in this assay.
  • the ribosome inactivation abilities of the SLT-lA::aLeishmania::KDEL cytotoxic protein is determined in a cell-free, in vitro protein translation as described above in the previous examples.
  • the inhibitory effect of the cytotoxic protein of this example on cell-free protein synthesis is significant.
  • the ICso of SLT-lA::aLeishmania: :KDEL on protein synthesis in this cell-free assay is approximately 0.1 -100 pM.
  • the cytotoxicity characteristics of SLT-lA::aLeishmania::KDEL are determined by the general cell-kill assay as described above in the previous examples using Leishmania antigen positive cells.
  • the selective cytotoxicity characteristics of SLT-lA::aLeishmania::KDEL are determined by the same general cell-kill assay using Leishmania antigen negative cells as a comparison to the Leishmania antigen positive cells.
  • the CD50 of the cytotoxic protein of this example is approximately 0.01-100 nM for Leishmania antigen positive cells depending on the cell line.
  • the CD50 of the cytotoxic protein is approximately 10-10,000 fold greater (less cytotoxic) for cells not expressing the Leishmania antigen on a cellular surface as compared to cells which do express the Leishmania antigen on a cellular surface.
  • Example 11 A Cytotoxic Protein Comprising a De-Immunized Shiga Toxin Effector Polypeptide and a Binding Region Derived from an
  • the Shiga toxin effector region is a de-immunized Shiga toxin effector polypeptide derived from the A subunit of Shiga-like Toxin 1 (SLT-1A) and comprising one or more de-immunizing amino acid substitutions described in the previous examples.
  • An immunoglobulin-type binding region aNeurotensin-Receptor is derived from the DARPinTM (GenBank Accession: 2P2C_R) or a monoclonal antibody (Ovigne J et al, Neuropeptides 32: 247-56 (1998)) which binds the human neurotensin receptor.
  • the neurotensin receptor is expressed by various cancer cells, such as breast cancer, colon cancer, lung cancer, melanoma, and pancreatic cancer cells.
  • the immunoglobulin-type binding region aNeurotensinR and Shiga toxin effector region are linked together, and a carboxy -terminal KDEL is added to form a protein.
  • a fusion protein is produced by expressing a polynucleotide encoding the neurotensin-receptor-binding protein SLT- lA::aNeurotensinR::KDEL. Expression of the SLT-lA::aNeurotensinR::KDEL cytotoxic protein is accomplished using either bacterial and/or cell-free, protein translation systems as described in the previous examples.
  • the binding characteristics of the cytotoxic protein of this example for neurotensin receptor positive cells and neurotensin receptor negative cells is determined by a fluorescence-based, flow-cytometry.
  • the Bmax for SLT- lA: :aNeurotensinR: :KDEL to neurotensin receptor positive cells is measured to be approximately 50,000-200,000 MFI with a KD within the range of 0.01 - 100 nM, whereas there is no significant binding to neurotensin receptor negative cells in this assay.
  • the ribosome inactivation abilities of the SLT- lA: :aNeurotensinR: :KDEL cytotoxic protein is determined in a cell- free, in vitro protein translation as described above in the previous examples.
  • the inhibitory effect of the cytotoxic protein of this example on cell-free protein synthesis is significant.
  • the ICso of SLT-lA: :aNeurotensinR: :KDEL on protein synthesis in this cell-free assay is approximately 0. 1 - 100 pM. Determining the Cytotoxicity of the Cytotoxic Protein SLT- lA: :aNeurotensinR: :KDEL Using a Cell-Kill Assay
  • the cytotoxicity characteristics of SLT- 1 A: :aNeurotensinR: :KDEL are determined by the general cell-kill assay as described above in the previous examples using neurotensin receptor positive cells.
  • the selective cytotoxicity characteristics of SLT- 1 A: :aNeurotensinR: :KDEL are determined by the same general cell-kill assay using neurotensin receptor negative cells as a comparison to the neurotensin receptor positive cells.
  • the CD50 of the cytotoxic protein of this example is approximately 0.01 - 100 nM for neurotensin receptor positive cells depending on the cell line.
  • the CD50 of the cytotoxic protein is approximately 10- 10,000 fold greater (less cytotoxic) for cells not expressing neurotensin receptor on a cellular surface as compared to cells which do express neurotensin receptor on a cellular surface. Determining Reductions in Antigenicity and/or Immunogenicity
  • mice Animal models are used to determine the in vivo effects of the cytotoxic protein SLT-lA::aNeurotensinR::KDEL on neoplastic cells.
  • Various mice strains are used to test the effect of the cytotoxic protein after intravenous administration on xenograft tumors in mice resulting from the injection into those mice of human neoplastic cells which express neurotensin receptors on their cell surfaces.
  • Example 12 A Cytotoxic Protein Comprising a De-Immunized Shiga Toxin Effector Polypeptide and a Binding Region Derived from an
  • the Shiga toxin effector region is a de-immunized Shiga toxin effector polypeptide derived from the A subunit of Shiga-like Toxin 1
  • the binding region aEGFR is derived from the AdNectinTM (GenBank Accession: 3QWQ_B), the AffibodyTM (GenBank Accession: 2KZI_A; U.S. patent 8,598, 113), or an antibody, all of which bind one or more human epidermal growth factor receptors.
  • the expression of epidermal growth factor receptors are associated with human cancer cells, such as, e.g., lung cancer cells, breast cancer cells, and colon cancer cells.
  • the immunoglobulin-type binding region aEGFR and Shiga toxin effector region are linked together, and a carboxy -terminal KDEL is added to form a protein.
  • a fusion protein is produced by expressing a polynucleotide encoding the EGFR binding protein SLT-lA::aEGFR::KDEL. Expression of the SLT- lA: :aEGFR: :KDEL cytotoxic protein is accomplished using either bacterial and/or cell-free, protein translation systems as described in the previous examples. Determining the In Vitro Characteristics of the Cytotoxic Protein SLT- lA: :otEGFR: :KDEL
  • the binding characteristics of the cytotoxic protein of this example for EGFR+ cells and EGFR- cells is determined by a fluorescence-based, flow- cytometry.
  • the Bmax for SLT-lA: :aEGFR::KDEL to EGFR+ cells is measured to be approximately 50,000-200,000 MFI with a KD within the range of 0.01 - 100 nM, whereas there is no significant binding to EGFR- cells in this assay.
  • the ribosome inactivation abilities of the SLT- 1 A: :aEGFR: :KDEL cytotoxic protein is determined in a cell-free, in vitro protein translation as described above in the previous examples.
  • the inhibitory effect of the cytotoxic protein of this example on cell-free protein synthesis is significant.
  • the ICso of SLT- lA: :aEGFR: :KDEL on protein synthesis in this cell-free assay is approximately 0. 1 - 100 pM.
  • cytotoxicity characteristics of SLT- 1 A: :aEGFR: :KDEL are determined by the general cell-kill assay as described above in the previous examples using EGFR+ cells.
  • the selective cytotoxicity is determined by the general cell-kill assay as described above in the previous examples using EGFR+ cells.
  • SLT- lA: :aEGFR: :KDEL characteristics of SLT- lA: :aEGFR: :KDEL are determined by the same general cell-kill assay using EGFR- cells as a comparison to the Leishmania antigen positive cells.
  • the CD50 of the cytotoxic protein of this example is
  • the CD50 of the cytotoxic protein is approximately 10- 10,000 fold greater (less cytotoxic) for cells not expressing EGFR on a cellular surface as compared to cells which do express EGFR on a cellular surface. Determining Reductions in Antigenicity and/or Immunogenicity
  • SLT-lA::aEGFR::KDEL The relative de-immunization of SLT-lA::aEGFR::KDEL is determined in relation to a wild-type Shiga toxin effector region polypeptide using western analyses, ELISA analyses, and murine models as described in Examples 4 and 6.
  • Example 13 A Cytotoxic Protein Comprising a De-Immunized Shiga Toxin Effector Polypeptide and a Binding Region Derived from the Antibody aCCR5
  • the Shiga toxin effector region is a de-immunized Shiga toxin effector polypeptide derived from the A subunit of Shiga-like Toxin 1 (SLT-1A) and comprising one or more de-immunizing amino acid substitutions described in the previous examples.
  • An immunoglobulin-type binding region aCCR5 is derived from a monoclonal antibody against human CCR5 (CD 195) (Bernstone L et al., Hybridoma 31 : 7-19 (2012)). CCR5 is predominantly expressed on T-cells, macrophages, dendritic cells, and microglia. In addition, CCR5 plays a role in the pathogenesis and spread of the Human
  • HIV Immunodeficiency Virus
  • the immunoglobulin-type binding region aCCR5 and Shiga toxin effector region are linked together, and a carboxy -terminal KDEL is added to form a protein.
  • a fusion protein is produced by expressing a polynucleotide encoding the aCCR5-binding protein SLT-lA::aCCR5: :KDEL. Expression of the SLT-lA::aCCR5::KDEL cytotoxic protein is accomplished using either bacterial and/or cell-free, protein translation systems as described in the previous examples. Determining the In Vitro Characteristics of the Cytotoxic Protein SLT- lA::otCCR5
  • the binding characteristics of the cytotoxic protein of this example for CCR5+ cells and CCR5- cells is determined by a fluorescence-based, flow- cytometry.
  • the B ma x for SLT- 1 A: :aCCR5 : :KDEL to CCR5+ positive cells is measured to be approximately 50,000-200,000 MFI with a KD within the range of 0.01-100 nM, whereas there is no significant binding to CCR5- cells in this assay.
  • the ribosome inactivation abilities of the SLT-lA::aCCR5::KDEL cytotoxic protein is determined in a cell-free, in vitro protein translation as described above in the previous examples.
  • the inhibitory effect of the cytotoxic protein of this example on cell-free protein synthesis is significant.
  • the ICso of SLT-lA::aCCR5::KDEL on protein synthesis in this cell-free assay is approximately 0.1-100 pM.
  • characteristics of SLT-lA::aCCR5::KDEL are determined by the same general cell-kill assay using CCR5- cells as a comparison to the CCR5+ cells.
  • the CD50 of the cytotoxic protein of this example is approximately 0.01-100 nM for CCR5+ cells depending on the cell line.
  • the CD50 of the cytotoxic protein is approximately 10-10,000 fold greater (less cytotoxic) for cells not expressing CCR5 on a cellular surface as compared to cells which do express CCR5 on a cellular surface.
  • SLT-lA::aCCR5::KDEL In vivo depletion of peripheral blood T lymphocytes in cynomolgus primates is observed after parenteral administration of different doses of SLT-lA::aCCR5::KDEL.
  • the use of SLT-lA::aCCR5::KDEL to block HIV infection is tested by giving an acute dose of SLT- lA::aCCR5::KDEL to non-human primates in order to severely deplete circulating T-cells upon exposure to a simian immunodeficiency virus (SIV) (see Sellier P et al, PLoS One 5: el0570 (2010)).
  • SIV simian immunodeficiency virus
  • Example 14 A Cytotoxic Protein Comprising a De-Immunized Shiga Toxin Effector Polypeptide and a Binding Region Derived from an Anti-Env Immunoglubulin Domain
  • the Shiga toxin effector region is a de-immunized Shiga toxin effector polypeptide derived from the A subunit of Shiga toxin (StxA) and comprising one or more de-immunizing amino acid substitutions described in the previous examples.
  • An immunoglobulin-type binding region aEnv is derived from existing antibodies that bind HIV envelope glycoprotein (Env), such as GP41, GP120, GP140, or GP160 (see e.g.
  • Envs are HIV surface proteins that are also displayed on the cell surfaces of HIV-infected cells during HIV replication. Although Envs are expressed in infected cells predominantly in endosomal compartments, sufficient amounts of Envs could be present on a cell surface to be targeted by a highly potent cytotoxic protein of the invention. In addition, Env-targeting cytotoxic proteins might bind HIV virions and enter newly infected cells during the fusion of virions with a host cell.
  • HIV displays a high rate of mutation it is preferable to use an immunoglobulin domain that binds a functional constrained part of an Env, such as shown by broadly neutralizing antibodies that bind Envs from multiple strains of HIV (van den Kerkhof T et al, Retrovirology 10: 102 (2013)). Because the Envs present on an infected cell's surface are believed to present sterically restricted epitopes (Chen W et al, J Virol 88: 1 125-39 (2014)), it is preferable to use smaller than 100 kD and ideally smaller than 25 kD, such as sdAbs or VHH domains.
  • the immunoglobulin-type binding region aEnv and Shiga toxin effector region are linked together, and a carboxy -terminal KDEL is added to form a cytotoxic protein.
  • a fusion protein is produced by expressing a polynucleotide encoding the ⁇ -binding protein SLT-lA::aEnv::KDEL. Expression of the SLT-lA::aEnv::KDEL cytotoxic protein is accomplished using either bacterial and/or cell-free, protein translation systems as described in the previous examples.
  • the binding characteristics of the cytotoxic protein of this example for Env+ cells and Env- cells is determined by a fluorescence-based, flow- cytometry.
  • the Bmax for SLT-lA::aEnv::KDEL to Env+ positive cells is measured to be approximately 50,000-200,000 MFI with a KD within the range of 0.01-100 nM, whereas there is no significant binding to Env- cells in this assay.
  • the ribosome inactivation abilities of the SLT-lA::aEnv::KDEL cytotoxic protein is determined in a cell-free, in vitro protein translation as described above in the previous examples.
  • the inhibitory effect of the cytotoxic protein of this example on cell-free protein synthesis is significant.
  • the IC50 of SLT-lA::aEnv: :KDEL on protein synthesis in this cell- free assay is
  • the cytotoxicity characteristics of SLT- 1 A: :aEnv: :KDEL are determined by the general cell-kill assay as described above in the previous examples using Env+ cells.
  • the selective cytotoxicity characteristics of SLT- lA::aEnv::KDEL are determined by the same general cell-kill assay using Env- cells as a comparison to the Env+ cells.
  • the CD50 of the cytotoxic protein of this example is approximately 0.01-100 nM for Env+ cells depending on the cell line and/or the HIV strain used to infect the cells to make them Env+.
  • the CD50 of the cytotoxic protein is approximately 10-10,000 fold greater (less cytotoxic) for cells not expressing Env on a cellular surface as compared to cells which do express Env on a cellular surface.
  • SLT- 1 A : aEnv : : KDEL to inhibit HIV infection is tested by administering SLT-lA::aEnv::KDEL to simian immunodeficiency virus (SIV) infected non-human primates (see Sellier P et al, PLoS One 5: el0570 (2010)).
  • SIV simian immunodeficiency virus
  • Example 15 A Cytotoxic Protein Comprising a De-Immunized Shiga Toxin Effector Polypeptide and a Binding Region Derived from the Antibody aUL18
  • the Shiga toxin effector region is a de-immunized Shiga toxin effector polypeptide derived from the A subunit of Shiga-like Toxin 1 (SLT-1A) and comprising one or more de-immunizing amino acid substitutions described in the previous examples.
  • An immunoglobulin-type binding region aUL18 is derived from an antibody generated, using techniques known in the art, to the cell-surface cytomegalovirus protein UL18, which is present on human cells infected with cytomegalovirus (Yang Z, Bjorkman P, Proc Natl Acad Sci USA 105: 10095-100 (2008)). The human cytomegalovirus infection is associated with various cancers and inflammatory disorders.
  • the immunoglobulin-type binding region aUL18 and Shiga toxin effector region are linked together, and a carboxy -terminal KDEL is added to form a protein.
  • a fusion protein is produced by expressing a polynucleotide encoding the aUL18-binding protein SLT-lA::aUL18: :KDEL. Expression of the SLT-lA::aUL18::KDEL cytotoxic protein is accomplished using either bacterial and/or cell-free, protein translation systems as described in the previous examples.
  • the binding characteristics of the cytotoxic protein of this example for cytomegalovirus protein UL18 positive cells and cytomegalovirus protein UL18 negative cells is determined by a fluorescence-based, flow-cytometry.
  • the Bmax for SLT-lA::aUL18::KDEL to cytomegalovirus protein UL18 positive cells is measured to be approximately 50,000-200,000 MFI with a KD within the range of 0.01-100 nM, whereas there is no significant binding to cytomegalovirus protein UL18 negative cells in this assay.
  • the ribosome inactivation abilities of the SLT-lA::aUL18: :KDEL cytotoxic protein is determined in a cell-free, in vitro protein translation as described above in the previous examples.
  • the inhibitory effect of the cytotoxic protein of this example on cell-free protein synthesis is significant.
  • the ICso of SLT-lA::aUL18::KDEL on protein synthesis in this cell-free assay is approximately 0.1-100 pM. Determining the Cytotoxicity of the Cytotoxic Protein SLT-lA::otUL18::KDEL Using a Cell-Kill Assay
  • the cytotoxicity characteristics of SLT-lA::aUL18::KDEL are determined by the general cell-kill assay as described above in the previous examples using cytomegalovirus protein UL18 positive cells.
  • the selective cytotoxicity characteristics of SLT-lA::aUL18::KDEL are determined by the same general cell-kill assay using cytomegalovirus protein UL18 negative cells as a comparison to the cytomegalovirus protein UL18 positive cells.
  • the CD50 of the cytotoxic protein of this example is approximately 0.01-100 nM for cytomegalovirus protein UL18 positive cells depending on the cell line.
  • the CD50 of the cytotoxic protein is approximately 10-10,000 fold greater (less cytotoxic) for cells not expressing the cytomegalovirus protein UL18 on a cellular surface as compared to cells which do express the cytomegalovirus protein UL18 on a cellular surface.
  • the Shiga toxin effector region is a de-immunized Shiga toxin effector polypeptide derived from the A subunit of Shiga-like Toxin 1 (SLT-1A), Shiga toxin (StxA), and/or Shiga-like Toxin 2 (SLT-2A) with any combination of B-cell epitope regions disrupted.
  • a binding region is derived from the immunoglobulin domain from the molecule chosen from column 1 of Table 12 and which binds the extracellular target biomolecule indicated in column 2 of Table 12.
  • the exemplary cytotoxic proteins of this example are optionally created with a carboxy-terminal KDEL-type signal motif and/or detection promoting agent(s) using reagents and techniques known in the art.
  • the exemplary cytotoxic proteins of this example are tested as described in the previous examples using cells expressing the appropriate extracellular target biomolecules.
  • the exemplary proteins of this example may be used, e.g., to diagnose and treat diseases, conditions, and/or disorders indicated in column 3 of Table 12.
  • immune disorders such as autoimmune disorders ipilimumab CD 152 T-cell related disorders and various cancers, such as leukemia, melanoma muromonab CD3 prevention of organ
  • natalizumab integrin a4 autoimmune disorders such as multiple sclerosis and Crohn's disease obinutuzumab CD20 B-cell cancers, such as lymphoma and leukemia, and B-cell related immune disorders, such as autoimmune disorders ocaratuzumab CD20 B-cell cancers, such as lymphoma and leukemia, and B-cell related immune disorders, such as autoimmune disorders ocrelizumab CD20 B-cell cancers, such as lymphoma and leukemia, and B-cell related immune disorders, such as autoimmune disorders ofatumumab CD20 B-cell cancers, such as lymphoma and leukemia, and B-cell related immune disorders, such as autoimmune disorders palivizumab F protein of respiratory treat respiratory syncytial syncytial virus virus virus
  • panitumumab EGFR various cancers such as colorectal cancer and head and neck cancer pertuzumab HER2/neu various cancers and tumors, such as breast cancer and colorectal cancer
  • cancer related disorders such as solid tumors rituximab CD20 B-cell cancers, such as lymphoma and leukemia, and B-cell related immune disorders, such as autoimmune disorders
  • ganitumab IGF-I various cancers golimumab TNF-a various cancers and immune disorders, such as rheumatoid arthritis, psoriatic arthritis, ankylosing spondylitis infliximab TNF-a various cancers and immune disorders, such as rheumatoid arthritis, ankylosing spondylitis, psoriatic arthritis, psoriasis, Crohn's disease, ulcerative colitis ixekizumab IL-17A various cancers and immune disorders, such as autoimmune diseases mepolizumab IL-5 various immune
  • disorders and cancers such as B-cell cancers nerelimomab TNF-a various cancers and immune disorders olokizumab IL6 various cancers and immune disorders ozoralizumab TNF-a inflammation perakizumab IL17A various cancers and immune disorders, such as arthritis
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Abstract

The present invention relates to Shiga toxin effector polypeptides with reduced antigenic and/or immunogenic potential. Immunogenicity can be a limitation for the repeated administration to mammals of proteins and polypeptides derived from Shiga toxins. The Shiga toxin effector polypeptides of the present invention have uses as components of therapeutics, diagnostics, and immunization materials. The cytotoxic proteins of the present invention have uses for selective killing of specific cell types and as therapeutics for the treatment of a variety of diseases, including cancers, immune disorders, and microbial infections. The proteins of the present invention also have uses for detecting specific cell types, collecting diagnostic information, and monitoring the treatment of a variety of diseases, such as, e.g., cancers, immune disorders, and microbial infections.

Description

DE-IMMUNIZED SHIGA TOXIN A SUBUNIT EFFECTOR POLYPEPTIDES FOR APPLICATIONS IN MAMMALS
FIELD OF THE INVENTION
[1] The present invention relates to de- immunized Shiga toxin effector polypeptides derived from A Subunits of naturally occurring Shiga toxins.
Polypeptides of the invention are beneficial alone or as components of molecules, e.g. therapeutics, for administration to mammals where reducing associated immune responses is desirable. For example, the polypeptides of this invention may be used as components of specifically targeted molecules, e.g. immunotoxins and ligand-toxin fusions, for the targeted killing of specific cell types. Proteins of the invention have uses as, e.g., components of therapeutics and diagnostics for the diagnosis, prognosis, and treatment of a variety of diseases, disorders and conditions, including cancers, tumors, immune disorders, and microbial infections.
BACKGROUND
[2] Shiga toxins have been synthetically engineered for medical applications by rational alterations to the toxin's structure, characteristics, and biological activities (see, e.g. US7713915, EP1051482, EP1727827, EP1945660;
applications: US2009/0156417 Al, EP2228383 Bl, EP2402367 Al,
US2013/0196928 Al, US2014/023198, US2014/023231, US61/951,1 10;
US61/951, 121, each of which is incorporated by reference herein in its entirety). Shiga toxin A Subunits are stable, enzymatically active, and cytotoxic even if truncated or fused to other protein domains (Haddad J et al, J Bacteriol 175:
4970-8 (1993); Al-Jaufy A et al, Infect Immun 62: 956-60 (1994); Al-Jaufy A et al, Infect Immun 63: 3073-8 (1995); LaPointe, J Biol Chem 280: 23310-18 (2005); Di R et al, Toxicon 57: 535-39 (201 1)). These Shiga toxin A Subunit- derived polypeptides may be linked or fused to immunoglobulin domains or receptor ligands through chemical conjugation or recombinant protein engineering in order to create cell-targeted therapeutic molecules. One aim of such molecular engineering is to design chimeric molecules with the dual functionality of: 1) delivering toxins to specific cell types or places within an organism after systemic administration; and 2) effectuating a targeted cytotoxicity to specific cells using potent cytotoxic mechanisms effective in eukaryotic cells.
[3] One of the main limitations of therapeutic applications involving synthetically engineered proteins from non-human sources is immunogenicity. Antigenicity and/or immunogenicity results from the ability of an antigenic epitope of a molecule to induce an antibody and/or immune response when that molecule is administered in vivo. Most therapeutic proteins are believed to induce an immune response of some sort, which ranges from production of low- level, low-affinity and transient antibodies like IgM to high-level, high-affinity IgG antibodies (Schellekens H, Clin Ther 24: 1720-30 (2002); Schellekens H, Nat Rev Drug Discov 1 : 457-62 (2002)). Unwanted immunogenicity of a therapeutic product could result in unfavorable consequences, such as a reduced efficacy, altered pharmacokinetics, general immune and hypersensitivity reactions, anaphylaxis, and anaphylactoid reactions (Buttel I et al, Biologicals 39: 100-9 (201 1)). For example, the production of neutralizing antibodies or anti-drug antibodies in a patient can limit the long-term effectiveness of repeated doses or chronic administration of a therapeutic.
[4] Because unwanted immune responses can pose significant safety and/or efficacy issue(s) for a therapeutic, minimizing antigenicity and/or
immunogenicity is often desirable when developing therapeutic proteins.
Unfortunately, at present and, despite extensive laboratory and clinical research, it is not possible to predict before administration to a patient the extent to which a novel therapeutic protein will be immunogenic (Descotes J, Gouraud A, Expert Opin Drug Metab Toxicol 4: 1537-49 (2008)). This is due in large part to both a lack of current understanding about and the heterogeneity of mechanisms of antibody generation by the adaptive immune systems of vertebrates. For example, analyses of antigen-antibody complexes have revealed no
determinative structural feature(s) of a generic epitope, except perhaps for a higher likelihood of exposed hydrophilic and bulky amino acids with high solvent accessible surface areas.
[5] Despite these difficulties, various strategies are presently utilized to reduce the immunogenic potential of a protein (see e.g. Onda M et al, Proc Natl Acad Sci USA 105: 1 131 1-6 (2008); Vallera D et al, Mol Cancer Ther 9: 1872- 83 (2010)). The immunogenic potential of a protein can be reduced by removing or disrupting epitopes likely to be recognized by the adaptive immune system. Epitope disruption or removal can be accomplished by mutation, e.g. truncation, deletion, or amino acid substitution, or humanization ( agata S, Pastan I, Adv Drug Deliv Rev 61 : 977-85 (2009); Baker M et al., Self Nonself \ : 314-22 (2010)).
[6] For de-immunization of a therapeutic molecule, priority is often given to identifying and disrupting B-lymphocyte (B-cell) antigenic epitopes likely to produce high affinity antibodies due to affinity maturation. After antigen activation, B-cells can differentiate into either plasma cells or memory cells. Activated B-cells can undergo class-switching to change from expressing low- affinity IgM and IgD antibodies to expressing a single Ig isotype, IgG, IgE, IgA, or IgD, which recognizes a discrete antigenic epitope (Klein U et al, Nat Rev Immunol 8: 22-33 (2008)). Activated B-cells expressing single Ig isotypes can undergo selection for those B-cells which produce antibodies with high-affinity to specific antigenic epitopes. Thus, the disruption of an epitope in a therapeutic may prevent, upon administration to a subject of the therapeutic, the production of high affinity antibodies that specifically bind that epitope as well as the formation of long-lived memory B-cells targeting that epitope.
[7] Currently there are no standard techniques for accurate and
comprehensive B-cell epitope prediction in a polypeptide (Sathish J et al, Nat Rev Drug Discov 12: 306-24 (2013)). B-cell epitopes can be identified by various empirical methods using a combination of mutagenesis and antibodies, immunization, or phage display screening of immunoglobulin libraries. Putative B-cell epitopes can be predicted using computational tools which scan for predicted linear and discontinuous epitopes in a given polypeptide sequence which may then be disrupted in attempts to silence them (Larsen et al,
Immunome Res 2: 2 (2006); El-Manzalawy et al, JMol Recognit 21 : 243-55 (2008); Sollner J et al, Immunome Res 4: 1 (2008); Bryson C et al, BioDrugs 24: 1-8 (2010); Yao B et al., PLoS One 8: e62249 (2013)). These computational B-cell epitope predictions are not highly accurate and thus must be verified experimentally (see Nagata, Adv Drug Deliv Rev 61 : 977-85 (2009)). Epitope disruption is often attempted by mutating charged and/or aromatic residues within putative B-cell epitopes to alanine residues (Onda M et al, J Immunol 177: 8822-34 (2006); ui W Qt al, Proc Natl Acad Sci USA 109: 11782-7 (2012); Yumura K et al, Protein Sci 22: 213-21 (2012)). Furthermore, the accurate mapping and disruption of all potential epitopes, while maintaining biotherapeutic activity, may be an elusive goal for larger proteins (Brauer F et al, Antimicrob Agents Chemother 57: 678-88 (2013)).
[8] Shiga toxins show promise for being engineered into useful products for therapeutic and diagnostic applications, but their potential immunogenicity may be an obstacle to uses in medical applications. Shiga toxins are bacterial proteins which are highly foreign to the human immune system. However, the antigenic and/or immunogenic sites within the A Subunits of Shiga toxins have not been systematically mapped. It would be desirable to have improved Shiga toxin A Subunit-derived polypeptides with reduced antigenicity and/or immunogenicity which retain sufficient Shiga toxin effector functions for medical applications, e.g., as components of various therapeutics involving targeted delivery of cytotoxicity to specific cell types.
SUMMARY OF THE INVENTION
[9] The present invention provides Shiga toxin effector polypeptides which have reduced antigenic and/or immunogenic potential in mammals (referred to herein as "de-immunized"). In addition, the present invention provides cytotoxic proteins and diagnostic proteins comprising de-immunized Shiga toxin effector polypeptides. De-immunized polypeptides derived from Shiga toxin A Subunits may be linked to one or more polypeptides that mediate cell targeting via specific extracellular binding interactions to enable the engineering of improved therapeutics for cell type specific targeting of cellular internalization and Shiga toxin cytotoxicity. The linking of detection promoting agents with de- immunized Shiga toxin effector region polypeptides enables the engineering of improved diagnostic molecules for detecting the presence of specific cell types. The polypeptides and proteins of the invention have uses for targeted cell killing, delivering exogenous materials into specific cell types, obtaining diagnostic information, and as therapeutics for the treatment of a variety of diseases, disorders, and conditions, including cancers, immune disorders, and microbial infections.
[10] A polypeptide of the invention comprises a Shiga toxin effector region comprising a polypeptide derived from the amino acid sequence of the A Subunit of at least one member of the Shiga toxin family with at least one predicted B-cell epitope removed or disrupted by mutation in such a way that at least one Shiga toxin effector function is retained.
[11] Certain embodiments of the polypeptides of the invention comprise a Shiga toxin effector region comprising a polypeptide derived from the amino acid sequence of the A Subunit of at least one member of the Shiga toxin family with at least one predicted B-cell epitope removed or disrupted by mutation in such a way that at least one Shiga toxin effector function is retained; and wherein an ectopic, MHC class I-restricted, T-cell epitope is not introduced by any B-cell epitope disruption. MHC class I-restricted, T-cell epitopes are known or can be predicted by the skilled worker. The term ectopic refers to MHC class I-restricted, T-cell epitopes which are not natively present in the polypeptide before said polypeptide was de-immunized, i.e. the parental polypeptide before one or more B-cell epitope was removed and/or disrupted.
[12] Certain embodiments of the invention provide polypeptides comprising a de-immunized Shiga toxin effector region comprising an amino acid sequence derived from an A Subunit of a member of the Shiga toxin Family, the Shiga toxin effector region comprising a disruption of at least one epitope region of the Shiga toxin A Subunit amino acid sequence selected from the group of natively positioned amino acid residues consisting of: 94-1 15 of SEQ ID NO: 1, SEQ ID NO:2, or SEQ ID O:3; 141-153 of SEQ ID O: l or SEQ ID O:2; 140-156 of SEQ ID O:3; 179-190 of SEQ ID O: l or SEQ ID O:2; 179-191 of SEQ ID NO:3; 204 of SEQ ID O:3; 205 of SEQ ID O: l or SEQ ID O:2; or 210-218 of SEQ ID NO:3; wherein the Shiga toxin effector region is capable of exhibiting a Shiga toxin effector function.
[13] Certain embodiments of the invention provide polypeptides comprising a de-immunized Shiga toxin effector region comprising an amino acid sequence derived from an A Subunit of a member of the Shiga toxin Family, the Shiga toxin effector region comprising a disruption of at least one epitope region of the Shiga toxin A Subunit amino acid sequence selected from the group of natively positioned amino acid residues consisting of: 94-1 15 of SEQ ID NO: 1, SEQ ID NO:2, or SEQ ID NO:3; 141-153 of SEQ ID NO: l or SEQ ID NO:2; 140-156 of SEQ ID NO:3; 179-190 of SEQ ID NO: l or SEQ ID NO:2; 179-191 of SEQ ID NO:3; 204 of SEQ ID NO:3; 205 of SEQ ID NO: l or SEQ ID NO:2; or 210-218 of SEQ ID NO:3; wherein the Shiga toxin effector region is capable of exhibiting a significant level of a Shiga toxin effector function.
[14] Certain embodiments of the invention provide polypeptides comprising a de-immunized Shiga toxin effector region comprising an amino acid sequence derived from an A Subunit of a member of the Shiga toxin Family, the Shiga toxin effector region comprising a disruption of at least one epitope region of the Shiga toxin A Subunit amino acid sequence selected the group of natively positioned amino acid residues consisting of: 94-1 15 of SEQ ID NO: 1, SEQ ID NO:2, or SEQ ID O:3; 141-153 of SEQ ID O: l or SEQ ID O:2; 140-156 of SEQ ID O:3; 179-190 of SEQ ID NO: 1 or SEQ ID NO:2; 179-191 of SEQ ID NO: 3; 204 of SEQ ID NO:3; 205 of SEQ ID NO: l or SEQ ID NO :2; or 210-218 of SEQ ID NO:3; wherein the Shiga toxin effector region is capable of a Shiga toxin effector function; and wherein the disruption is not of a single epitope region and does not consist solely of the amino acid residue substitution selected from the group consisting of: S96Y of SEQ ID NO: 1 or SEQ ID NO:2; Yl 14S of SEQ ID NO: 1 or SEQ ID NO:2; R179A of SEQ ID NO: 1 or SEQ ID NO:2; R179H of SEQ ID NO: 1 or SEQ ID NO:2; LI 85A of SEQ ID NO: 1 or SEQ ID NO:2; Rl 88A of SEQ ID NO: 1 or SEQ ID NO:2; R205A of SEQ ID NO: 1 or SEQ ID NO:2; R179A/R188A of SEQ ID NO: l ; or SEQ ID NO:2; or A188V of SEQ ID NO :3.
[15] Certain embodiments of the invention provide polypeptides comprising a de-immunized Shiga toxin effector region comprising an amino acid sequence derived from an A Subunit of a member of the Shiga toxin Family, the Shiga toxin effector region comprising a disruption of at least one epitope region of the Shiga toxin A Subunit amino acid sequence selected from the group of natively positioned amino acid residues consisting of: 94-1 15 of SEQ ID NO: 1, SEQ ID NO:2, or SEQ ID NO:3; 141-153 of SEQ ID NO: l or SEQ ID NO:2; 140-156 of SEQ ID NO:3; 179-190 of SEQ ID NO: l or SEQ ID NO:2; 179-191 of SEQ ID NO: 3; 204 of SEQ ID NO:3; 205 of SEQ ID NO: l or SEQ ID NO :2; or 210-218 of SEQ ID NO:3; wherein the Shiga toxin effector region is capable of exhibiting a significant level of a Shiga toxin effector function; and wherein the disruption is not of a single epitope region and does not consist solely of the amino acid residue substitution selected from the group consisting of: S96Y of SEQ ID NO: 1 or SEQ ID NO:2; Yl 14S of SEQ ID NO: 1 or SEQ ID NO:2; NO:2; L185A of SEQ ID NO: l or SEQ ID NO:2; R188A of SEQ ID NO: l or SEQ ID NO:2; R205A of SEQ ID NO: l or SEQ ID NO:2; R179A/R188A of SEQ ID NO: l ; or SEQ ID NO:2; or A188V of SEQ ID NO:3.
[16] Certain embodiments of the invention provide polypeptides comprising a de-immunized Shiga toxin effector region comprising an amino acid sequence derived from an A Subunit of a member of the Shiga toxin Family, the Shiga toxin effector region comprising a disruption of at least one epitope region of the Shiga toxin A Subunit amino acid sequence selected from the group of natively positioned amino acid residues consisting of: 1-15 of SEQ ID NO: 1 or SEQ ID NO:2; 3-14 of SEQ ID NO:3; 26-37 of SEQ ID NO:3; 27-37 of SEQ ID NO: l or SEQ ID NO:2; 39-48 of SEQ ID NO: 1 or SEQ ID NO:2; 42-48 of SEQ ID NO:3; 53-66 of SEQ ID NO: l, SEQ ID NO:2, or SEQ ID NO:3; wherein the Shiga toxin effector region is capable of exhibiting a a Shiga toxin effector function; and wherein the Shiga toxin effector region comprises no amino terminus truncation overlapping with a disrupted epitope region of the Shiga toxin A Subunit from which derived which overlaps with a disrupted epitope region.
[17] Certain embodiments of the invention provide polypeptides comprising a de-immunized Shiga toxin effector region comprising an amino acid sequence derived from an A Subunit of a member of the Shiga toxin Family, the Shiga toxin effector region comprising a disruption of at least one epitope region of the Shiga toxin A Subunit amino acid sequence selected from the group of natively positioned amino acid residues consisting of: 1-15 of SEQ ID NO: 1 or SEQ ID NO:2; 3-14 of SEQ ID NO:3; 26-37 of SEQ ID NO:3; 27-37 of SEQ ID NO: l or SEQ ID NO:2; 39-48 of SEQ ID NO: 1 or SEQ ID NO:2; 42-48 of SEQ ID NO:3; 53-66 of SEQ ID NO: l, SEQ ID NO:2, or SEQ ID NO:3; wherein the Shiga toxin effector region is capable of exhibiting a significant level of a Shiga toxin effector function; and wherein the Shiga toxin effector region comprises no amino terminus truncation overlapping with a disrupted epitope region of the Shiga toxin A Subunit from which derived which overlaps with a disrupted epitope region.
[18] Certain embodiments of the invention provide polypeptides comprising a de-immunized Shiga toxin effector region comprising an amino acid sequence derived from an A Subunit of a member of the Shiga toxin Family, the Shiga toxin effector region comprising a disruption of at least one epitope region of the Shiga toxin A Subunit amino acid sequence selected from the group of natively positioned amino acid residues consisting of: 1-15 of SEQ ID NO: 1 or SEQ ID NO:2; 3-14 of SEQ ID O:3; 26-37 of SEQ ID O:3; 27-37 of SEQ ID O: l or SEQ ID NO:2; 39-48 of SEQ ID NO: 1 or SEQ ID NO:2; 42-48 of SEQ ID NO:3; 53-66 of SEQ ID NO: l, SEQ ID NO:2, or SEQ ID NO:3; wherein the Shiga toxin effector region is capable of exhibiting a Shiga toxin effector function; wherein the disruption is not of a single epitope region and does not consist solely of the amino acid residue substitution R63W of SEQ ID NO: 1 or SEQ ID NO:2; and wherein the Shiga toxin effector region comprises no amino terminus truncation overlapping with a disrupted epitope region of the Shiga toxin A Subunit from which derived which overlaps with a disrupted epitope region.
[19] Certain embodiments of the invention provide polypeptides comprising a de-immunized Shiga toxin effector region comprising an amino acid sequence derived from an A Subunit of a member of the Shiga toxin Family, the Shiga toxin effector region comprising a disruption of at least one epitope region of the Shiga toxin A Subunit amino acid sequence selected from the group of natively positioned amino acid residues consisting of: 240-260 of SEQ ID NO:3; 243- 257 of SEQ ID NO: 1 or SEQ ID NO:2; 254-268 of SEQ ID NO: 1 or SEQ ID NO:2; 262-278 of SEQ ID NO:3; 281-297 of SEQ ID NO:3; and 285-293 of SEQ ID NO: 1 or SEQ ID NO:2; wherein the Shiga toxin effector region is capable of exhibiting a Shiga toxin effector function; and wherein the Shiga toxin effector region comprises no carboxy terminus truncation overlapping with a disrupted epitope region of the of the Shiga toxin A Subunit from which derived which overlaps with a disrupted epitope region.
[20] Certain embodiments of the invention provide polypeptides comprising a de-immunized Shiga toxin effector region comprising an amino acid sequence derived from an A Subunit of a member of the Shiga toxin Family, the Shiga toxin effector region comprising a disruption of at least one epitope region of the Shiga toxin A Subunit amino acid sequence selected from the group of natively positioned amino acid residues consisting of: 240-260 of SEQ ID NO:3; 243- 257 of SEQ ID NO: 1 or SEQ ID NO:2; 254-268 of SEQ ID NO: 1 or SEQ ID NO:2; 262-278 of SEQ ID NO:3; 281-297 of SEQ ID NO:3; and 285-293 of SEQ ID NO: 1 or SEQ ID NO:2; wherein the Shiga toxin effector region is capable of exhibiting a Shiga toxin effector function; wherein the disruption is not of a single epitope region and does not solely consist of the amino acid residue substitution selected from the group consisting of: R248H of SEQ ID NO: l or SEQ ID NO:2; A250V of SEQ ID NO: l or SEQ ID NO:2; R251H of SEQ ID NO: 1 or SEQ ID NO:2; A253G of SEQ ID NO: 1 or SEQ ID NO:2; S254T of SEQ ID NO: 1 or SEQ ID NO:2; C261A of SEQ ID NO: 1 or SEQ ID NO:2; R289K of SEQ ID NO: 1 or SEQ ID NO:2; R248H and R251H of SEQ ID NO: 1 or SEQ ID NO:2; A253G and S254T of SEQ ID NO: 1 or SEQ ID NO:2; the deletion of S247-M252 of SEQ ID NO: l; S246F of SEQ ID NO:3; A282V of SEQ ID NO:3; 129 IV of SEQ ID NO:3; S246F/I291V of SEQ ID NO:3; and wherein the Shiga toxin effector region comprises no carboxy terminus truncation overlapping with a disrupted epitope region of the of the Shiga toxin A Subunit from which derived which overlaps with a disrupted epitope region.
[21] In certain further embodiments, the de-immunized Shiga toxin effector region polypeptide of the invention comprises an epitope disruption which comprises a deletion of at least one amino acid within an epitope region provided herein. In certain further embodiments, a polypeptide of the invention comprises an epitope disruption which comprises an insertion of at least one amino acid within an epitope region provided. In certain further embodiments, the polypeptides comprise a disruption which comprises an inversion or other rearrangement of amino acids, wherein at least one inverted amino acid is within the epitope region provided. In certain further embodiments, the polypeptides comprise an epitope disruption which comprises an amino acid residue mutation, such as a single amino acid substitution to a non-standard amino acid or an amino acid with a chemically modified side chain.
[22] In certain embodiments, the de-immunized Shiga toxin effector regions comprise an epitope disruption which comprises an amino acid residue substitution within an epitope region provided herein. In certain further embodiments, the polypeptides comprise at least one substitution to an amino acid selected from the group consisting of: A, G, V, L, I, P, C, M, F, S, D, N, Q, H, and K. In certain further embodiments, the polypeptide comprise a substitution selected from the group consisting of: D to A, D to G, D to V, D to L, D to I, D to F, D to S, D to Q, E to A, E to G, E to V, E to L, E to I, E to F, E to S, E to Q, E to N, E to D, E to M, E to R, G to A, H to A, H to G, H to V, H to L, H to I, H to F, H to M, K to A, K to G, K to V, K to L, K to I, K to M, K to H, L to A, L to G, N to A, N to G, N to V, N to L, N to I, N to F, P to A, P to G, P to F, R to A, R to G, R to V, R to L, R to I, R to F, R to M, R to Q, R to S, R to K, R to H, S to A, S to G, S to V, S to L, S to I, S to F, S to M, T to A, T to G, T to V, T to L, T to I, T to F, T to M, T to S, Y to A, Y to G, Y to V, Y to L, Y to I, Y to F, and Y to M.
[23] In certain embodiments, the de-immunized Shiga toxin effector regions comprise a disruption which comprises an amino acid residue substitution within an epitope region, wherein the substitution occurs at the natively positioned amino acid selected from the group of natively positioned amino acid residues consisting of: 1 of SEQ ID NO: 1 or SEQ ID NO:2; 4 of SEQ ID NO: 1, SEQ ID NO:2, or SEQ ID NO:3; 8 of SEQ ID NO:l, SEQ ID NO:2, or SEQ ID NO:3; 9 of SEQIDNO:l, SEQIDNO:2, orSEQIDNO:3; 11 of SEQ ID NO: 1, SEQ ID NO:2, or SEQ ID NO:3; 33 of SEQ ID NO:l or SEQ ID NO:2; 43 of SEQ ID NO: 1 or SEQ ID NO:2; 45 of SEQ ID NO: 1 or SEQ ID NO:2; 47 of SEQ ID NO:l or SEQ ID NO:2; 48 of SEQ ID NO:l, SEQ ID NO:2, or SEQ ID NO:3; 49 of SEQ ID NO: 1 or SEQ ID NO:2; 53 of SEQ ID NO: 1 or SEQ ID NO:2; 55 of SEQ ID NO: 1 or SEQ ID NO:2; 58 of SEQ ID NO: 1, SEQ ID NO:2, or SEQ ID NO:3; 59 of SEQ ID NO: 1, SEQ ID NO:2, or SEQ ID NO:3; 60 of SEQ ID NO: 1 or SEQ ID NO:2; 61 of SEQ ID NO: 1 or SEQ ID NO:2; 62 of SEQ ID NO:l or SEQ ID NO:2; 94 of SEQ ID NO:l, SEQ ID NO:2, or SEQ ID NO:3; 96 of SEQ ID NO:l, SEQ ID NO:2, or SEQ ID NO:3; 109 of SEQ ID NO:l, SEQIDNO:2, orSEQIDNO:3; 110 of SEQ ID NO: 1 orSEQIDNO:2; 112 of SEQ IDNO:l, SEQ IDNO:2, or SEQ IDNO:3; SE 147 of SEQ IDNO:l, SEQ ID NO:2, or SEQ ID NO:3; 179 of SEQ ID NO:l, SEQ ID NO:2, or SEQ ID NO:3; 180 of SEQ IDNO:l or SEQIDNO:2; 181 of SEQ IDNO:l or SEQ ID NO:2; 183 of SEQ ID NO:l, SEQ ID NO:2, or SEQ ID NO:3; 184 of SEQ ID NO:l, SEQIDNO:2, orSEQIDNO:3; 185 of SEQIDNO:l orSEQIDNO:2; 186 of SEQ IDNO:l, SEQ IDNO:2, or SEQ IDNO:3; 187 ofSEQIDNO:l or SEQ ID NO:2; 188 of SEQ ID NO: 1 or SEQ ID NO:2; 189 of SEQ ID NO: 1 or SEQ ID NO:2; 204 of SEQ ID NO:3; 205 of SEQ ID NO: 1 or SEQ ID NO:2; 247 of SEQ ID NO: 1 or SEQ ID NO:2; 247 of SEQ ID NO:3; 248 of SEQ ID NO:l or SEQ ID O:2; 250 of SEQ ID NO:3; 251 of SEQ ID O:l or SEQ ID NO:2; 264 of SEQ ID NO:l, SEQ ID NO:2, or SEQ ID NO:3; 265 of SEQ ID NO: 1 or SEQ ID NO:2; and 286 of SEQ ID NO: 1 or SEQ ID NO:2. In certain further embodiments, the polypeptides comprise an epitope disruption which comprises an amino acid residue substitution within an epitope region, wherein the substitution is to any non-conservative amino acid and the substitution occurs at the amino acid residue selected from the group of natively positioned amino acid residues consisting of: 1 of SEQ ID NO: 1 or SEQ ID NO:2; 4 of SEQ ID NO:l, SEQ ID NO:2, or SEQ ID NO:3; 8 of SEQ ID NO:l, SEQ ID NO:2, or SEQ ID NO:3; 9 of SEQ ID NO:l, SEQ ID NO:2, or SEQ ID NO:3; 11 of SEQ IDNO:l, SEQ ID NO:2, or SEQ IDNO:3; 33 of SEQ ID NO:l or SEQ ID NO:2; 43 of SEQ ID NO: 1 or SEQ ID NO:2; 45 of SEQ ID NO: 1 or SEQ ID NO:2; 47 of SEQ ID NO: 1 or SEQ ID NO:2; 48 of SEQ ID NO: 1, SEQ ID NO:2, or SEQ ID NO:3; 49 of SEQ ID NO:l or SEQ ID NO:2; 53 of SEQ ID NO: 1 or SEQ ID NO:2; 55 of SEQ ID NO: 1 or SEQ ID NO:2; 58 of SEQ ID NO: 1, SEQ ID NO:2, or SEQ ID NO:3; 59 of SEQ ID NO: 1, SEQ ID NO:2, or SEQ IDNO:3;60 of SEQ IDNO:l or SEQ IDNO:2;61 of SEQ IDNO:l or SEQ ID NO:2; 62 of SEQ ID NO:l or SEQ ID NO:2; 94 of SEQ ID NO:l, SEQ ID NO:2, or SEQ ID NO:3; 96 of SEQ ID NO: 1, SEQ ID NO:2, or SEQ ID NO:3; 109 of SEQ ID NO:l, SEQ ID NO:2, or SEQ ID NO:3; 110 of SEQ ID NO:l or SEQ ID NO:2; 112 of SEQ ID NO:l, SEQ ID NO:2, or SEQ ID NO:3; SE 147 of SEQ IDNO:l, SEQ IDNO:2, or SEQ IDNO:3; 179 of SEQ ID NO: 1, SEQ ID NO:2, or SEQ ID NO:3; 180 of SEQ ID NO: 1 or SEQ ID NO:2; 181 of SEQ ID NO: 1 or SEQ IDNO:2; 183 of SEQ IDNO:l, SEQ IDNO:2, or SEQIDNO:3; 184 of SEQ ID NO:l, SEQ ID NO:2, or SEQ ID NO:3; 185 of SEQ IDNO:l or SEQ ID NO:2; 186 of SEQ ID NO:l, SEQ IDNO:2, or SEQ IDNO:3; 187 of SEQ IDNO:l or SEQ IDNO:2; 188 of SEQ ID NO: 1 or SEQ IDNO:2; 189 of SEQ IDNO:l or SEQ IDNO:2; 204 of SEQ ID NO:3; 205 of SEQ ID NO: 1 or SEQ ID NO:2; 247 of SEQ ID NO: 1 or SEQ ID NO:2; 247 of SEQ ID NO:3; 248 of SEQ ID NO:l or SEQ ID NO:2; 250 of SEQ ID NO:3; 251 of SEQ ID NO: 1 or SEQ ID NO:2; 264 of SEQ ID NO: 1, SEQ ID NO:2, or SEQ ID NO:3; 265 of SEQ ID NO: 1 or SEQ ID NO:2; and 286 of SEQ ID NO: 1 or SEQ ID NO:2. A non-conservative amino acid substitution is a substitution of one amino acid with another amino acid which has one or more markedly different biochemical properties, such as, e.g., charged to uncharged, polar to hydrophobic, and bulky to small. In certain further embodiments, the polypeptides comprise an epitope disruption which comprises an amino acid residue substitution within an epitope region, wherein the substitution occurs at the natively positioned amino acid residue and the substitution is to an amino acid selected from the group consisting of: Kl to A, G, V, L, I, F, M and H; T4 to A, G, V, L, I, F, M, and S; S8 to A, G, V, I, L, F, and M; T9 to A, G, V, I, L,
F, M, and S; S9 to A, G, V, L, I, F, and M; Kl 1 to A, G, V, L, I, F, M and H; S33 to A, G, V, L, I, F, and M; S45 to A, G, V, L, I, F, and M; T45 to A, G, V, L, I, F, and M; D47 to A, G, V, L, I, F, S, and Q; N48 to A, G, V, L, and M; L49 to A or G; D53 to A, G, V, L, I, F, S, and Q; R55 to A, G, V, L, I, F, M, Q, S, K, and H; D58 to A, G, V, L, I, F, S, and Q; P59 to A, G, and F; E60 to A, G, V, L, I, F, S, Q, N, D, M, and R; E61 to A, G, V, L, I, F, S, Q, N, D, M, and R; G62 to A; D94 to A, G, V, L, I, F, S, and Q; S96 to A, G, V, I, L, F, and M; SI 09 to A, G, V, I, L, F, and M; T109 to A, G, V, I, L, F, M, and S; Gl 10 to A; SI 12 to A,
G, V, L, I, F, and M; G147 to A; R179 to A, G, V, L, I, F, M, Q, S, K, and H; T180 to A, G, V, L, I, F, M, and S; T181 to A, G, V, L, I, F, M, and S; D183 to A, G, V, L, I, F, S, and Q; D184 to A, G, V, L, I, F, S, and Q; S186 to A, G, V, I, L, F, and M; G187 to A; R188 to A, G, V, L, I, F, M, Q, S, K, and H; S189 to A, G, V, I, L, F, and M; R204 to A, G, V, L, I, F, M, Q, S, K, and H; R205 to A, G, V, L, I, F, M, Q, S, K and H; S247 to A, G, V, I, L, F, and M; Y247 to A, G, V, L, I, F, and M; R248 to A, G, V, L, I, F, M, Q, S, K, and H; R250 to A, G, V, L, I, F, M, Q, S, K, and H; R251 to A, G, V, L, I, F, M, Q, S, K, and H; D264 to A, G, V, L, I, F, S, and Q; G264 to A; and T286 to A, G, V, L, I, F, M, and S.
[24] For certain embodiments, the polypeptides of the invention comprise the de-immunized Shiga toxin effector region derived from amino acids 75 to 251 of SEQ ID NO: 1, SEQ ID NO:2, or SEQ ID NO:3. In certain further embodiments, the polypeptides of the invention comprise a de-immunized Shiga toxin effector region derived from amino acids 1 to 251 of SEQ ID NO: 1, SEQ ID NO:2, or SEQ ID NO:3; and/or amino acids 1 to 261 of SEQ ID NO:l, SEQ ID NO:2, or SEQ ID NO:3. In certain embodiments, the polypeptides of the invention comprise the de-immunized Shiga toxin effector region derived from amino acids 1 to 241 SEQ ID NO:l, SEQ ID NO:2, or SEQ ID NO:3. [25] For certain embodiments, the polypeptides of the invention comprise the de-immunized Shiga toxin effector region comprising or consisting essentially of any one of SEQ ID NOs: 4-52.
[26] Certain embodiments of the invention provide a protein comprising a binding region for cell targeting linked to a de-immunized Shiga-toxin-Subunit- A derived region which exhibits one or more Shiga toxin effector function(s), e.g. cytotoxic activity. The proteins of the invention comprise a de-immunized Shiga toxin effector region comprising a polypeptide of the invention and a binding region comprising one or more polypeptides which are capable of specifically binding at least one extracellular target biomolecule.
[27] In certain embodiments of the proteins of the present invention, the binding region comprises a polypeptide selected from the group consisting of: a complementary determining region 3 (CDR3) fragment constrained FR3-CDR3- FR4 (FR3-CDR3-FR4) polypeptide, single-domain antibody fragment (sdAb), nanobody, heavy-chain antibody domain derived from a camelid (VHH
fragment), heavy-chain antibody domain derived from a cartilaginous fish, immunoglobulin new antigen receptors (IgNARs), VNAR fragment, single-chain variable fragment (scFv), antibody variable fragment (Fv), antigen-binding fragment (Fab), Fd fragment, small modular immunopharmaceutical (SMIP) domain, fibronection-derived 10th fibronectin type III domain (10Fn3) (e.g. monobody), tenacsin type III domain (e.g. TNfn3), ankyrin repeat motif domain (ARD), low-density-lipoprotein-receptor-derived A-domain (A domain of LDLR or LDLR-A), lipocalin (anticalin), Kunitz domain, Protein-A-derived Z domain, gamma-B crystalline-derived domain (Affilin), ubiquitin-derived domain, Sac7d-derived polypeptide, Fyn-derived SH2 domain (affitin), miniprotein, C- type lectin-like domain scaffold, engineered antibody mimic, and any genetically manipulated counterparts of any of the foregoing that retain binding
functionality.
[28] In certain embodiments of the present invention, upon administration of the de-immunized cytotoxic protein of the present invention to a cell physically coupled with an extracellular target biomolecule of the binding region of the cytotoxic protein, the cytotoxic protein is capable of causing death of the cell.
[29] In certain embodiments of the present invention, upon administration of the de-immunized cytotoxic protein of the present invention to two different populations of cell types with respect to the presence of an extracellular target biomolecule, the cytotoxic protein is capable of causing cell death to the cell- types physically coupled with an extracellular target biomolecule of its binding region at a CD50 at least three times or less than the CD50 to cell types which are not physically coupled with an extracellular target biomolecule of the cytotoxic protein's binding region.
[30] In certain embodiments of the proteins of the present invention, the binding region is designed or selected by its ability to bind an extracellular target biomolecule selected from the group consisting of: CD20, CD22, CD40, CD79, CD25, CD30, HER2/neu/ErbB2, EGFR, EpCAM, EphB2, prostate-specific membrane antigen, Cripto, CDCP 1, endoglin, fibroblast activated protein, Lewis-Y, CD19, CD21, CS1/ SLAMF7, CD33, CD52, EpCAM, CEA, gpA33, Mucins, TAG-72, carbonic anhydrase IX, folate binding protein, ganglioside GD2, ganglioside GD3, ganglioside GM2, ganglioside Lewis-Y2, VEGFR, Alpha Vbeta3, Alpha5betal, ErbBl/EGFR, Erb3, c-MET, IGF1R, EphA3,
TRAIL-Rl, TRAIL-R2, RANKL, FAP, Tenascin, CD64, mesothelin, BRCA1, MART- 1/MelanA, gplOO, tyrosinase, TRP-1, TRP-2, MAGE-1, MAGE-3, GAGE- 1/2, BAGE, RAGE, NY-ESO-1, CDK-4, beta-catenin, MUM-1, caspase- 8, KIAA0205, HPVE6, SART-1, PRAME, carcinoembryonic antigen, prostate specific antigen, prostate stem cell antigen, human aspartyl (asparaginyl) beta- hydroxylase, EphA2, HER3/ErbB-3, MUC1, MART- 1/MelanA, gplOO, tyrosinase associated antigen, HPV-E7, Epstein-Barr Virus antigens, Bcr-Abl, alpha-fetoprotein antigen, 17-A1, bladder tumor antigen, CD38, CD15, CD23, CD52, CD53, CD88, CD129, CD183, CD191, CD193, CD244, CD294, CD305, C3AR, FceRIa, galectin-9, mrp-14, siglec-8, siglec-10, CD49d, CD 13, CD44, CD54, CD63, CD69, CD123, CD193, TLR4, FceRIa, IgE, CD107a, CD203c, CD14, CD 15, CD33, CD64, CD68, CD80, CD86, CD105, CD 115, F4/80, ILT-3, Galectin-3, CDl la-c, GITRL, MHC Class II, CD284-TLR4, CD107-Mac3, CD195-CCR5, HLA-DR, CD16/32, CD282-TLR2, CDl lc, CD123, and any immunogenic fragment of any of the foregoing.
[31] In certain embodiments, the proteins of the invention comprise a carboxy -terminal endoplasmic reticulum retention/retrieval signal motif of a member of the KDEL family. In certain further embodiments, the proteins of the present invention comprise a carboxy-terminal endoplasmic reticulum retention/retrieval signal motif is selected from the group consisting of: KDEL, HDEF, HDEL, RDEF, RDEL, WDEL, YDEL, HEEF, HEEL, KEEL, REEL, KAEL, KCEL, KFEL, KGEL, KHEL, KLEL, KNEL, KQEL, KREL, KSEL, KVEL, KWEL, KYEL, KEDL, KIEL, DKEL, FDEL, KDEF, KKEL, HADL, HAEL, HIEL, HNEL, HTEL, KTEL, HVEL, NDEL, QDEL, REDL, RNEL, RTDL, RTEL, SDEL, TDEL, and SKEL.
[32] For certain embodiments, the protein of the present invention comprises a binding region and a de-immunized Shiga toxin effector region which are physically oriented within the protein such that said binding region is not located adjacent to the amino-terminus of the Shiga toxin effector region.
[33] For certain embodiments, the proteins of the present invention comprise a Shiga toxin effector region derived from amino acids 75 to 251 of SEQ ID NO: l, SEQ ID NO:2, or SEQ ID NO:3. Certain further embodiments provide proteins in which the Shiga toxin effector region is derived from amino acids 1 to 251 of SEQ ID NO: l, SEQ ID NO:2, or SEQ ID NO:3; and/or amino acids 1 to 261 of SEQ ID NO: 1, SEQ ID NO:2, or SEQ ID NO:3. In certain embodiments, the proteins of the present invention comprise a Shiga toxin effector region is derived from amino acids 1 to 241 SEQ ID NO: l, SEQ ID NO:2, or SEQ ID NO:3.
[34] For certain embodiments, the proteins of the invention comprise the de- immunized Shiga toxin effector region comprising or consisting essentially of any one of SEQ ID NOs: 4-52.
[35] For certain embodiments, the protein of the present invention comprises or consists essentially of SEQ ID NO:53, SEQ ID NO:54, SEQ ID NO:55, SEQ ID NO:56, SEQ ID NO:57, SEQ ID NO:58, or SEQ ID NO:59.
[36] In certain embodiments, the proteins of the invention comprise a de- immunized Shiga toxin effector region which further comprises a mutation relative to a naturally occurring A Subunit of a member of the Shiga toxin family that changes the enzymatic activity of the Shiga toxin effector region, the mutation selected from at least one amino acid residue deletion or substitution, such as, e.g., A231E, R75A, Y77S, Y114S, E167D, R170A, R176K and/or W203A in SEQ ID NO: 1, SEQ ID NO:2, or SEQ ID NO:3. In certain further embodiments, the proteins of the present invention comprise a mutation which reduces or eliminates catalytic activity but retains at least one other Shiga toxin effector function(s).
[37] The present invention also provides pharmaceutical compositions comprising a polypeptide and/or protein of the invention and at least one pharmaceutically acceptable excipient or carrier; and the use of such a protein or a composition comprising it in methods of the invention as further described herein.
[38] Beyond the polypeptides, proteins, and compositions of the present invention, polynucleotides capable of encoding a polypeptide comprising a de- immunized Shiga toxin effector region or protein of the present invention comprising a de-immunized Shiga toxin effector region of the invention are within the scope of the present invention, as well as expression vectors which comprise a polynucleotide of the invention and host cells comprising an expression vector of the invention. Host cells comprising an expression vector may be used, e.g., in methods for producing a polypeptide and/or protein of the invention, or a polypeptide component or fragment thereof, by recombinant expression.
[39] Additionally, the present invention provides methods of selectively killing cell(s) comprising the step of contacting a cell(s) with a protein of the invention or a pharmaceutical composition comprising such a protein of the invention. In certain embodiments, the step of contacting the cell(s) occurs in vitro. In certain other embodiments, the step of contacting the cell(s) occurs in vivo.
[40] The present invention further provides methods of treating diseases, disorders, and/or conditions in patients in need thereof comprising the step of administering to a patient in need thereof a therapeutically effective amount of a composition comprising a de-immunized Shiga toxin effector region polypeptide of the invention, a polypeptide and/or protein comprising it, or a composition comprising any of the foregoing (e.g., a pharmaceutical composition). In certain embodiments, the disease, disorder, or condition to be treated using this method of the invention is selected from: a cancer, tumor, immune disorder, or microbial infection. In certain embodiments of this method, the cancer to be treated is selected from the group consisting of: bone cancer, breast cancer, central/peripheral nervous system cancer, gastrointestinal cancer, germ cell cancer, glandular cancer, head-neck cancer, hematological cancer, kidney- urinary tract cancer, liver cancer, lung/pleura cancer, prostate cancer, sarcoma, skin cancer, and uterine cancer. In certain embodiments of this method, the immune disorder to be treated is an immune disorder associated with a disease selected from the group consisting of: amyloidosis, ankylosing spondylitis, asthma, Crohn's disease, diabetes, graft rejection, graft-versus-host disease, Hashimoto's thyroiditis, hemolytic uremic syndrome, HIV-related diseases, lupus erythematosus, multiple sclerosis, polyarteritis, psoriasis, psoriatic arthritis, rheumatoid arthritis, scleroderma, septic shock, Sjorgren's syndrome, ulcerative colitis, and vasculitis.
[41] Among certain embodiments of the present invention is a composition comprising a de-immunized Shiga toxin effector region polypeptide of the invention, a polypeptide and/or protein comprising it, or a composition comprising any of the foregoing, for the treatment or prevention of a cancer, tumor, immune disorder, or microbial infection. Among certain embodiments of the present invention is the use of a composition of matter of the invention in the manufacture of a medicament for the treatment or prevention of a cancer, tumor, immune disorder, or microbial infection.
[42] Certain embodiments of the proteins of the present invention may be used to deliver one or more additional exogenous materials into a cell physically coupled with an extracellular target biomolecule of the protein of the present invention. Additionally, the present invention provides a method for delivering exogenous material to the inside of a cell(s) comprising contacting the cell(s), either in vitro or in vivo, with a protein, pharmaceutical composition, and/or diagnostic composition of the present invention. The present invention further provides a method for delivering exogenous material to the inside of a cell(s) in a patient in need thereof, the method comprising the step of administering to the patient a protein of the present invention, wherein the target cell(s) is physically coupled with an extracellular target biomolecule of the protein of the present invention.
[43] Among certain embodiments of the present invention is the use of a compound (e.g. a polypeptide or protein) of the invention and/or composition (e.g. a pharmaceutical composition or diagnostic composition) of the invention in the diagnosis, prognosis, or characterization of a disease, disorder, or condition.
[44] Among certain embodiments of the present invention is a diagnostic composition comprising a de-immunized Shiga toxin effector region polypeptide of the invention, a polypeptide and/or protein comprising it, or a composition comprising any of the foregoing, and a detection promoting agent for the collection of information, such as diagnostically useful information about a cell type, tissue, organ, disease, disorder, condition, or patient.
[45] Among certain embodiments of the present invention is the method of detecting a cell using a protein and/or diagnostic composition of the invention comprising the steps of contacting a cell with said protein and/or diagnostic composition and detecting the presence of said protein and/or diagnostic composition. In certain embodiments, the step of contacting the cell(s) occurs in vitro. In certain embodiments, the step of contacting the cell(s) occurs in vivo. In certain embodiments, the step of detecting the cell(s) occurs in vitro. In certain embodiments, the step of detecting the cell(s) occurs in vivo.
[46] For example, a diagnostic composition of the invention may be used to detect a cell in vivo by administering to a mammalian subject a composition comprising protein of the present invention which comprises a detection promoting agent and then detecting the presence of the protein of the present invention either in vitro or in vivo. The information collected may regard the presence of a cell physically coupled with an extracellular target of the binding region of the protein of the present invention and may be useful in the diagnosis, prognosis, characterization, and/or treatment of a disease, disorder, or condition. Certain compounds (e.g. polypeptides and proteins) of the invention, compositions (e.g. pharmaceutical compositions and diagnostic compositions) of the invention, and methods of the invention may be used to determine if a patient belongs to a group that responds to a pharmaceutical composition of the invention.
[47] Certain embodiments of the polypeptides of the present invention may be utilized as an immunogen or as a component of an immunogen for the immunization and/or vaccination of a mammal. [48] Among certain embodiments of the present invention are kits comprising a composition of matter of the present invention, and optionally, instructions for use, additional reagent(s), and/or pharmaceutical delivery device(s).
[49] These and other features, aspects and advantages of the present invention will become better understood with regard to the following description, appended claims, and accompanying figures. The aforementioned elements of the invention may be individually combined or removed freely in order to make other embodiments of the invention, without any statement to object to such combination or removal hereinafter.
BRIEF DESCRIPTION OF THE FIGURES
[50] Figure 1 shows the general arrangement of exemplary de-immunized polypeptides and cytotoxic proteins.
[51] Figure 2 shows that the D58A substitution in a de-immunized Shiga toxin effector region effectively disrupted the epitope recognized by pAb2 under denaturing conditions and reduced the antigenicity of the polypeptide comprising a Shiga toxin effector region.
[52] Figure 3 shows that the D58A substitution in the context of multiple epitope region disruption variants of de-immunized Shiga toxin effector regions effectively disrupted the epitope recognized by pAb2 under denaturing conditions and reduced the antigenicity of the polypeptide a Shiga toxin effector region.
[53] Figure 4 shows that multiple-epitope-region-disruption variants of de- immunized Shiga toxin effector regions disrupted the epitopes recognized by pAb2 and mAbl under denaturing conditions. These multiple-epitope-region- disruption variants have reduced antigenicity as compared to a polypeptide comprising the parental, wild-type, Shiga toxin effector region.
[54] Figure 5 shows that multiple-epitope-region-disruption variants of de- immunized Shiga toxin effector regions effectively disrupted the epitopes recognized by pAb2 and/or mAbl under denaturing conditions. These multiple- epitope-region-disruption variants have reduced antigenicity as compared to a polypeptide comprising the parental, wild-type, Shiga toxin effector region.
[55] Figure 6 shows that a de-immunized Shiga toxin effector region comprising multiple epitope-region disruptions resulted in a very effective disruption of the epitope recognized by mAbl under native protein folding conditions. This multiple-epitope-region-disruption variant had reduced antigenicity as compared to a polypeptide comprising the parental, wild-type, Shiga toxin effector region.
[56] Figure 7 shows that a de-immunized Shiga toxin effector region comprising multiple epitope-region disruptions resulted in reduced, in vivo, antibody response(s) by a mammalian immune system. This multiple-epitope- region-disruption variant had reduced immunogenicity as compared to a polypeptide comprising the parental, wild-type, Shiga toxin effector region.
DETAILED DESCRIPTION
[57] The present invention is described more fully hereinafter using illustrative, non-limiting embodiments, and references to the accompanying figures. This invention may, however, be embodied in many different forms and should not be construed as to be limited to the embodiments set forth below. Rather, these embodiments are provided so that this disclosure is thorough and conveys the scope of the invention to those skilled in the art.
[58] In order that the present invention may be more readily understood, certain terms are defined below. Additional definitions may be found within the detailed description of the invention.
[59] As used in the specification and the appended claims, the terms "a," "an" and "the" include both singular and the plural referents unless the context clearly dictates otherwise.
[60] As used in the specification and the appended claims, the term "and/or" when referring to two species, A and B, means at least one of A and B. As used in the specification and the appended claims, the term "and/or" when referring to greater than two species, such as A, B, and C, means at least one of A, B, or C, or at least one of any combination of A, B, or C (with each species in singular or multiple possibility).
[61] Throughout this specification, the word "comprise" or variations such as "comprises" or "comprising" will be understood to imply the inclusion of a stated integer (or components) or group of integers (or components), but not the exclusion of any other integer (or components) or group of integers (or components). [62] Throughout this specification, the term "including" is used to mean "including but not limited to." "Including" and "including but not limited to" are used interchangeably.
[63] The term "amino acid residue" or "amino acid" includes reference to an amino acid that is incorporated into a protein, polypeptide, or peptide. The term "polypeptide" includes any polymer of amino acids or amino acid residues. The term "polypeptide sequence" refers to a series of amino acids or amino acid residues which physically comprise a polypeptide. A "protein" is a
macromolecule comprising one or more polypeptides chains. A "peptide" is a small polypeptide of sizes less than a total of 15-20 amino acid residues. The term "amino acid sequence" refers to a series of amino acids or amino acid residues which physically comprise a peptide or polypeptide depending on the length. Unless otherwise indicated, polypeptide and protein sequences disclosed herein are written from left to right representing their order from an amino terminus to a carboxy terminus.
[64] The terms "amino acid," "amino acid residue," "amino acid sequence," or "polypeptide sequence" includes naturally occurring amino acids and, unless otherwise limited, also include known analogs of natural amino acids that can function in a similar manner as naturally occurring amino acids, such as selenocysteine, pyrrolysine, N-formylmethionine, gamma-carboxyglutamate, hydroxyprolinehypusine, pyroglutamic acid, and selenomethionine. The amino acids referred to herein are described by shorthand designations as follows in Table A:
TABLE A. Amino Acid Nomenclature
Name 3-letter 1-letter
Alanine Ala A
Arginine Arg R
Asparagine Asn N
Aspartic Acid or Aspartate Asp D
Cysteine Cys C
Glutamic Acid or Glutamate Glu E
Glutamine Gin Q
Glycine Gly G
Histidine His H
Isoleucine He I
Leucine Leu L
Lysine Lys K
Methionine Met M Phenylalanine Phe F
Proline Pro P
Serine Ser S
Threonine Thr T
Tryptophan Trp W
Tyrosine Tyr Y
Valine Val V
[65] The phrase "conservative substitution" with regard to a polypeptide, refers to a change in the amino acid composition of the polypeptide that does not substantially alter the function and structure of the overall polypeptide (see Creighton, Proteins: Structures and Molecular Properties (W. H. Freeman and Company, New York (2nd ed., 1992)).
[66] As used herein, the terms "expressed," "expressing," or "expresses" and grammatical variants thereof refer to translation of a polynucleotide or nucleic acid into a polypeptide or protein. The expressed polypeptide or proteins may remain intracellular, become a component of the cell surface membrane or be secreted into an extracellular space.
[67] As used herein, the symbol "a" is shorthand for an immunoglobulin-type binding region capable of binding to the biomolecule following the symbol. The symbol "a" is used to refer to the functional characteristic of an
immunoglobulin-type binding region based on its capability of binding to the biomolecule following the symbol.
[68] The symbol means the polypeptide regions before and after it are physically linked together to form a continuous polypeptide.
[69] As used in the specification, the symbol "/" when located between two amino acid residue substitutions means the amino acid residue substitutions on either side of the "/" or comprised within the same molecule.
[70] For purposes of the present invention, the phrase "derived from" means the polypeptide region comprises amino acid sequences originally found in a protein and may now comprise additions, deletions, truncations, or other alterations from the original sequence such that overall function and structure are substantially conserved.
[71] For purposes of the present invention, the term "effector" means providing a biological activity, such as cytotoxicity, biological signaling, enzymatic catalysis, subcellular routing, and/or intermolecular binding resulting in the recruit of a factor(s) and/or an allosteric effect(s).
[72] For purposes of the present invention, a Shiga toxin effector function is a biological activity conferred by a polypeptide region derived from a Shiga toxin A Subunit. Non-limiting examples of Shiga toxin effector functions include cellular internalization, subcellular routing, catalytic activity, and cytotoxicity. Non-limiting examples of Shiga toxin catalytic activities include ribosome inactivation, protein synthesis inhibition, N-glycosidase activity,
polynucleotide:adenosine glycosidase activity, RNAase activity, and DNAase activity. RIPs can depurinate nucleic acids, polynucleosides, polynucleotides, rRNA, ssDNA, dsDNA, mRNA (and poly A), and viral nucleic acids (Barbieri L et al, Biochem J286: 1-4 (1992); Barbieri L et al, Nature 372: 624 (1994); Ling J et al, FEBS Lett 345: 143-6 (1994); Barbieri L et al, Biochem J 319: 507-13 (1996); Roncuzzi L, Gasperi-Campani A, FEBS Lett 392: 16-20 (1996); Stirpe F et al, FEBS Lett 382: 309-12 (1996); Barbieri L et al, Nucleic Acids Res 25: 518-22 (1997); Wang P, Turner N, Nucleic Acids Res 27: 1900-5 (1999);
Barbieri L et al, Biochim Biophys Acta 1480: 258-66 (2000); Barbieri L et al, J Biochem 128: 883-9 (2000); Bagga S et al, J Biol Chem 278: 4813-20 (2003); Picard D et al., J Biol Chem 280: 20069-75 (2005)). Some RIPs show antiviral activity and superoxide dismutase activity (Erice A et al, Antimicrob Agents
Chemother 37: 835-8 (1993); Au T et al, FEBSLett All : 169-72 (2000); Parikh B, Turner N, Mini Rev Med Chem 4: 523-43 (2004); Sharma N et al, Plant Physiol 134: 171-81 (2004)). Shiga toxin catalytic activities have been observed both in vitro and in vivo. Assays for Shiga toxin effector activity can measure various activities, such as, e.g., protein synthesis inhibitory activity, depurination activity, inhibition of cell growth, cytotoxicity, supercoiled DNA relaxation activity, and/or nuclease activity.
[73] The term "selective cytotoxicity" with regard to the cytotoxic activity of a cytotoxic protein refers to the relative levels of cytotoxicity between a targeted cell population and a non-targeted bystander cell population, which can be expressed as a ratio of the half- maximal cytotoxic concentration (CD50) for a targeted cell type over the CD50 for an untargeted cell type to show
preferentiality of cell killing of the targeted cell type. [74] As used herein, the retention of Shiga toxin effector function refers to a level of Shiga toxin functional activity, as measured by an appropriate quantitative assay with reproducibility, comparable to a wild-type Shiga toxin effector polypeptide control. For ribosome inhibition, retained Shiga toxin effector function is exhibiting an ICso of 10,000 pM or less. For cytotoxicity in a target positive cell kill assay, retained Shiga toxin effector function is exhibiting a CD50 of 1,000 nM or less, depending on the cell type and its expression of the appropriate extracellular target biomolecule.
[75] As used herein, "de-immunized" means reduced antigenic and/or immunogenic potential after administration to a mammal. This includes a reduced antigenic and/or immunogenic potential overall despite the introduction of one or more new epitopes.
Introduction
[76] The present invention provides improved polypeptides derived from A Subunits of members of the Shiga toxin family with reduced immunogenic potential. These improved Shiga toxin effector polypeptides may be utilized in various compositions, e.g. cytotoxic therapeutics, therapeutic delivery agents, diagnostic molecules, and immunization materials.
[77] Despite the attractiveness of using Shiga toxins as components of therapeutics, bacterial toxins tend to be immunogenic to mammals. Unwanted immunogenicity in protein therapeutics has resulted in reduced efficacy, unpredictable pharmacokinetics, and undesirable immune responses that limit dosages and repeat administrations. Although there is a need for molecules comprising de-immunized Shiga-toxin-derived polypeptides that have reduced immunogenic potential to help avoid unwanted immune responses, there exists no predictable method to successfully identify and remove internal B-cell epitopes while maintaining Shiga toxin effector function(s).
[78] Although some antigenic and/or immunogenic epitopes might be removed by truncation, the main challenge is silencing epitopes within the Shiga toxin polypeptide's effector domains, e.g. its enzymatic domain, while retaining the desired Shiga toxin effector functions, e.g., potent ribosome inhibition and directing subcellular routing. While these internal epitopes may be diminished or abolished by mutation and/or chemical modification, the challenge is to do so while preserving Shiga toxin effector functions. It is a significant challenge to disrupt antigenic sites by amino acid substitution in a protein while preserving protein function because functionally constrained residues and structures must be maintained and certain positions do not tolerate certain amino acid substitutions without impacting protein structure, stability, and/or function (see Cantor J et al, Methods in Enzymology 502: Ch. 12 pp. 291-301 (2012)).
[79] Extensive empirical experimentation on Shiga toxin derived polypeptide regions was performed to arrive at the present invention. As described in more detail in the Examples, amino acid substitutions were created in predicted B-cell epitopes, and the resulting polypeptides were tested for retention of desired
Shiga toxin effector functions. The antigenicity and/or immunogenicity of each epitope is predicted to be reduced or eliminated by the amino acid substitutions provided, which in turn reduces the overall antigenicity and/or immunogenicity of any compositions of matter comprising at least one provided epitope disruption. The de-immunized Shiga toxin effector polypeptides which were identified as having reduced immunogenic potential while maintaining Shiga toxin function(s), were not predictable a priori, despite attempts at de- immunization of distantly related bacterial protein toxins, such as Pseudomonas exotoxin A.
[80] Polypeptides comprising de-immunized Shiga toxin effector regions of the invention may be used as components of recombinant immunotoxins and ligand-toxin fusions for the targeted killing of specific cell types and the treatment of a variety of diseases, including cancers, immune disorders, and microbial infections. Additionally, the polypeptides of the invention may be used as components of cell-type specific internalizing molecules for the precise delivery of exogenous materials, such as detection promoting agents for diagnostic information gathering. Further, the polypeptides of the invention, independently or as components of Shiga holotoxins, may be used in
immunization materials designed to avoid antibody creation to specific epitopes while eliciting immune responses to Shiga toxins. I. The General Structure of Shiga Toxin Effector Polypeptides and Proteins of the Present Invention
[81] The present invention provides various polypeptides comprising Shiga toxin effector regions with reduced immunogenic potential but which retain Shiga toxin effector functionality(s), such as cellular internalization, subcellular routing, catalytic activity, and cytotoxicity. A polypeptide of the invention comprises a Shiga toxin effector region comprising a disruption of at least one epitope region described herein. A protein of the invention comprises a de- immunized Shiga toxin effector region and a binding region comprising one or more polypeptides capable of specifically binding at least one extracellular target biomolecule.
[82] The Shiga toxin family of protein toxins is composed of various naturally occurring toxins that are structurally and functionally related, e.g., Shiga toxin, Shiga-like toxin 1 , and Shiga-like toxin 2 (Johannes L, R5mer W, Nat Rev Microbiol 8: 105-16 (2010)). Members of the Shiga toxin family share the same overall structure and mechanism of action (Engedal, N et al, Microbial Biotech 4: 32-46 (201 1)). For example, Stx, SLT-1 and SLT-2 display indistinguishable enzymatic activity in cell free systems (Head S et al, J Biol Chem 266: 3617-21 (1991); Tesh V et al, Infect Immun 61 : 3392-402 (1993); Brigotti M et al, Toxicon 35: 1431-1437 (1997)).
A. De-Immunized Shiga Toxin Effector Region Polypeptides
[83] For purposes of the present invention, the phrase "Shiga toxin effector region" refers to a polypeptide region derived from a Shiga toxin A Subunit of a member of the Shiga toxin family that is capable of exhibiting at least one Shiga toxin function. Shiga toxin functions include, e.g., cell entry, lipid membrane deformation, directing subcellular routing, avoiding degradation, catalytically inactivating ribosomes, effectuating cytotoxicity, and effectuating cytostatic effects.
[84] As used herein, the retention of "significant" Shiga toxin effector function refers to a level of Shiga toxin functional activity, as measured by an appropriate quantitative assay with reproducibility comparable to a wild-type Shiga toxin effector polypeptide control. For in vitro ribosome inhibition, significant Shiga toxin effector function is exhibiting an ICso of 300 pM or less depending on the source of the ribosomes (e.g. bacteria, archaea, or eukaryote (algae, fungi, plants, or animals)). This is significantly greater inhibition as compared to the approximate IC50 of 100,000 pM for the catalytically inactive SLT-1A 1-251 double mutant (Y77S, E167D). For cytotoxicity in a target positive cell kill assay in laboratory cell culture, significant Shiga toxin effector function is exhibiting a CD50 of 100, 50, or 30 nM or less, depending on the cell line and its expression of the appropriate extracellular target biomolecule. This is significantly greater cytotoxicity to the appropriate target cell line as compared to SLT-1A alone, without a cell targeting binding region, which has a CD50 of 100- 10,000 nM, depending on the cell line.
[85] For some samples, accurate values for either IC50 or CD50 might be unobtainable due to the inability to collect the required data points for an accurate curve fit. Inaccurate IC50 and/or CD50 values should not be considered when determining significant Shiga toxin effector function activity. Data insufficient to accurately fit a curve as described in the analysis of the data from exemplary Shiga toxin effector function assays, such as, e.g., assays described in the Examples, should not be considered as representative of actual Shiga toxin effector function. For example, theoretically neither an IC50 nor CD50 can be determined if greater than 50% ribosome inhibition or cell death, respectively, does not occur in a concentration series for a given sample.
[86] The failure to detect activity in Shiga toxin effector function may be due to improper expression, polypeptide folding, and/or polypeptide stability rather than a lack of cell entry, subcellular routing, and/or enzymatic activity. Assays for Shiga toxin effector functions may not require much polypeptide of the invention to measure significant amounts of Shiga toxin effector function activity. To the extent that an underlying cause of low or no effector function is determined empirically to relate to protein expression or stability, one of skill in the art may be able to compensate for such factors using protein chemistry and molecular engineering techniques known in the art, such that a Shiga toxin functional effector activity may be restored and measured. As examples, improper cell based expression may be compensated for by using different expression control sequences; improper polypeptide folding and/or stability may benefit from stabilizing terminal sequences, or compensatory mutations in non- effector regions which stabilize the three dimensional structure of the protein, etc. When new assays for individual Shiga toxin functions become available, de-immunized Shiga toxin effector polypeptides may be analyzed for any level of those Shiga toxin effector functions, such as a being within 1000-fold or 100- fold or less the activity of a wild-type Shiga toxin effector polypeptide or exhibiting 3 -fold to 30-fold or greater activity as compared to a functional knockout Shiga toxin effector polypeptide.
[87] Certain Shiga toxin effector functions are not easily measurable, e.g. subcellular routing functions. Currently there is no routine, quantitative assay to distinguish whether the failure of a de-immunized Shiga toxin effector polypeptide to be cytotoxic is due to improper subcellular routing, but at a time when tests are available, de-immunized Shiga toxin effector polypeptides may be analyzed for any significant level of subcellular routing as compared to the appropriate wild-type Shiga toxin effector region.
[88] It should be noted that even if the cytotoxicity of a Shiga toxin effector polypeptide is reduced relative to wild-type, in practice, applications using attenuated de-immunized Shiga toxin effector polypeptides may be equally or more effective than those using wild-type Shiga toxin effector polypeptides because the reduced antigenicity and/or immunogenicity might offset the reduced cytotoxicity, such as, e.g., by allowing higher dosages or more repeated administrations. Wild-type Shiga toxin effector polypeptides are very potent, being able to kill with only one molecule reaching the cytosol or perhaps 40 molecules being internalized. De-immunized Shiga toxin effector polypeptides with even considerably reduced Shiga toxin effector functions, such as, e.g., subcellular routing or cytotoxicity, as compared to wild-type Shiga toxin effector polypeptides may still be potent enough for practical applications involving targeted cell killing and/or specific cell detection.
[89] The Shiga toxin family encompasses true Shiga toxin (Stx) isolated from S. dysenteriae serotype 1, Shiga-like toxin 1 variants (SLT1 or Stxl or SLT-1 or Slt-I) isolated from serotypes of enterohemorrhagic E. coli, and Shiga-like toxin 2 variants (SLT2 or Stx2 or SLT-2) isolated from serotypes of
enterohemorrhagic E. coli. SLT1 differs by only one residue from Stx, and both have been referred to as Verocytotoxins or Verotoxins (VTs) (O'Brien, Curr Top Microbiol Immunol 180: 65-94 (1992)). Although SLT1 and SLT2 variants are only about 53-60% similar to each other at the amino acid sequence level, they share mechanisms of enzymatic activity and cytotoxicity common to the members of the Shiga toxin family (Johannes, Nat Rev Microbiol 8: 105-16 (2010)). Over 39 different Shiga toxins have been described, such as the defined subtypes Stxla, Stxlc, Stxld, and Stx2a-g (Scheutz F et al, J Clin Microbiol 50: 2951-63 (2012)). Members of the Shiga toxin family are not naturally restricted to any bacterial species because Shiga-toxin-encoding genes can spread among bacterial species via horizontal gene transfer (Strauch E et al., Infect Immun 69: 7588-95 (2001); Zhaxybayeva O, Doolittle W, Curr Biol 21 : R242-6 (2011)). As an example of interspecies transfer, a Shiga toxin was discovered in a strain of A. haemolyticus isolated from a patient (Grotiuz G et al, J Clin Microbiol 44: 3838-41 (2006)). Once a Shiga toxin encoding polynucleotide enters a new subspecies or species, the Shiga toxin amino acid sequence is presumed to be capable of developing slight sequence variations due to genetic drift and/or selective pressure while still maintaining a mechanism of cytotoxicity common to members of the Shiga toxin family (see Scheutz, J Clin Microbiol 50: 2951-63 (2012)).
[90] The polypeptides of the invention comprise Shiga toxin effector regions derived from an A Subunit of a member of the Shiga toxin family with at least one putative epitope region disrupted in order to reduce the antigenic and/or immunogenic potential of the polypeptides after administration to a mammal. The term "disrupted" or "disruption" as used herein with regard to an epitope region refers to the deletion of at least one amino acid in an epitope region, inversion of two or more amino acids where at least one of the inverted amino acids is in an epitope region, insertion of at least one amino acid in an epitope region, and mutation of at least one amino acid in an epitope region. An epitope region disruption by mutation includes amino acid substitutions with nonstandard amino acids and/or non-natural amino acids. Epitope regions may alternatively be disrupted by mutations comprising the modification of an amino acid by the addition of a covalently-linked chemical structure which masks at least one amino acid in an epitope region, see, e.g. PEGylation (see Zhang C et al, BioDrugs 26: 209-15 (2012) and small molecule adjuvants (Flower D, Expert Opin Drug Discov 7: 807-17 (2012)).
[91] Certain epitope regions and disruptions are indicated herein by reference to specific amino acid positions of native Shiga toxin A Subunits provided in the Sequence Listing, noting that naturally occurring Shiga toxin A Subunits may comprise precursor forms containing signal sequences of about 22 amino acids at their amino-terminals which are removed to produce mature Shiga toxin A Subunits and are recognizable to the skilled worker. Further, certain epitope region disruptions are indicated herein by reference to specific amino acids (e.g. S for a serine residue) natively present at specific positions within native Shiga toxin A Subunits (e.g. S33 for the serine residue at position 33 from the amino terminus) followed by the amino acid with which that residue has been substituted in the particular mutation under discussion (e.g. S33I represents the amino acid substitution of isoleucine for serine at amino acid residue 33 from the amino terminus).
[92] Certain embodiments of the invention provide polypeptides comprising a Shiga toxin effector region comprising an amino acid sequence derived from an A Subunit of a member of the Shiga toxin Family, the Shiga toxin effector region comprising a disruption of at least one epitope region provided herein (see e.g. Tables 1, 2, and 3). In certain embodiments, a de- immunized Shiga toxin effector region polypeptide of the invention may comprise or consist essentially of full-length Shiga toxin A Subunit (e.g. SLT-1A (SEQ ID NO: l), StxA (SEQ ID NO:2), or SLT-2A (SEQ ID NO:3)) comprising at least one disruption of the amino acid sequence selected from the group of natively positioned amino acids consisting of: 1-15 of SEQ ID NO: 1 or SEQ ID NO:2; 3-14 of SEQ ID O:3; 26-37 of SEQ ID NO:3; 27-37 of SEQ ID NO: l or SEQ ID NO:2; 39-48 of SEQ ID NO: l or SEQ ID NO:2; 42-48 of SEQ ID NO:3; 53- 66 of SEQ ID O: l, SEQ ID O:2, or SEQ ID O:3; 94-1 15 of SEQ ID O: l, SEQ ID O:2, or SEQ ID O:3; 141-153 of SEQ ID NO: 1 or SEQ ID NO:2; 140-156 of SEQ ID NO:3; 179-190 of SEQ ID NO: l or SEQ ID NO:2; 179-191 of SEQ ID NO:3; 204 of SEQ ID NO:3; 205 of SEQ ID NO: l or SEQ ID NO:2; 210-218 of SEQ ID NO:3; 240-258 of SEQ ID NO:3; 243-257 of SEQ ID NO: 1 or SEQ ID NO:2; 254-268 of SEQ ID NO: 1 or SEQ ID NO:2; 262-278 of SEQ ID NO:3; 281-297 of SEQ ID NO:3; and 285-293 of SEQ ID NO: l or SEQ ID NO:2, or the equivalent position in a conserved Shiga toxin effector polypeptide and/or non-native Shiga toxin effector polypeptide sequence.
[93] In certain embodiments, a Shiga toxin effector region polypeptide of the invention may comprise or consist essentially of a truncated Shiga toxin A Subunit. Truncations of Shiga toxin A Subunits might result in the deletion of entire epitope regions without affecting toxin effector catalytic activity and cytotoxicity. The smallest Shiga toxin A Subunit fragment exhibiting significant enzymatic activity is a polypeptide composed of residues 75-247 of StxA (Al- Jaufy, Infect Immun 62: 956-60 (1994)). Truncating the carboxy-terminus of SLT-1A, StxA, or SLT-2A to amino acids 1-251 removes two predicted B-cell epitope regions, two predicted CD4 positive (CD4+) T-cell epitopes, and a predicted discontinuous B-cell epitope. Truncating the amino-terminus of SLT- 1A, StxA, or SLT-2A to 75-293 removes at least three predicted B-cell epitope regions and three predicted CD4+ T-cell epitopes. Truncating both amino- and carboxy -terminals of SLT-1A, StxA, or SLT-2A to 75-251 deletes at least five predicted B-cell epitope regions, four putative CD4+ T-cell epitopes, and one predicted discontinuous B-cell epitope.
[94] In certain embodiments, a Shiga toxin effector region polypeptide of the invention may comprise or consist essentially of a full-length or truncated Shiga toxin A Subunit with at least one mutation, e.g. deletion, insertion, inversion, or substitution, in a provided epitope region. In certain further embodiments, the polypeptides comprise a disruption which comprises a deletion of at least one amino acid within the epitope region. In certain further embodiments, the polypeptides comprise a disruption which comprises an insertion of at least one amino acid within the epitope region. In certain further embodiments, the polypeptides comprise a disruption which comprises an inversion of amino acids, wherein at least one inverted amino acid is within the epitope region. In certain further embodiments, the polypeptides comprise a disruption which comprises a mutation, such as an amino acid substitution to a non-standard amino acid or an amino acid with a chemically modified side chain. Numerous examples of single amino acid substitutions are provided in the Examples.
[95] In certain embodiments, the Shiga toxin effector region polypeptides of the invention may comprise or consist essentially of a full-length or truncated Shiga toxin A Subunit with one or more mutations as compared to the native sequence which comprises at least one amino acid substitution selected from the group consisting of: A, G, V, L, I, P, C, M, F, S, D, N, Q, H, and K. In certain further embodiments, the polypeptide may comprise or consist essentially of a full-length or truncated Shiga toxin A Subunit with a single mutation as compared to the native sequence wherein the substitution is selected from the group consisting of: D to A, D to G, D to V, D to L, D to I, D to F, D to S, D to Q, E to A, E to G, E to V, E to L, E to I, E to F, E to S, E to Q, E to N, E to D, E to M, E to R, G to A, H to A, H to G, H to V, H to L, H to I, H to F, H to M, K to A, K to G, K to V, K to L, K to I, K to M, K to H, L to A, L to G, N to A, N to G, N to V, N to L, N to I, N to F, P to A, P to G, P to F, R to A, R to G, R to V, R to L, R to I, R to F, R to M, R to Q, R to S, R to K, R to H, S to A, S to G, S to V, S to L, S to I, S to F, S to M, T to A, T to G, T to V, T to L, T to I, T to F, T to M, T to S, Y to A, Y to G, Y to V, Y to L, Y to I, Y to F, and Y to M.
[96] In certain embodiments, the Shiga toxin effector region polypeptides of the invention comprise or consist essentially of a full-length or truncated Shiga toxin A Subunit with one or more mutations as compared to the native amino acid residue sequence which comprises at least one amino acid substitution within an epitope region, wherein at least one substitution occurs at the natively positioned group of amino acids selected from the group consisting of: 1 of SEQ ID NO: 1 or SEQ ID NO:2; 4 of SEQ ID NO: 1, SEQ ID NO:2, or SEQ ID NO:3; 8 of SEQ ID NO: 1, SEQ ID NO:2, or SEQ ID NO:3; 9 of SEQ ID NO: 1, SEQ ID NO:2, or SEQ ID NO:3; 11 of SEQ ID NO: 1, SEQ ID NO:2, or SEQ ID NO:3; 33 of SEQ ID NO: 1 or SEQ ID NO:2; 43 of SEQ ID NO: 1 or SEQ ID NO:2; 45 of SEQ ID NO: 1 or SEQ ID NO:2; 47 of SEQ ID NO: 1 or SEQ ID NO:2; 48 of SEQ ID NO:l, SEQ ID NO:2, or SEQ ID NO:3; 49 of SEQ ID NO: 1 or SEQ ID NO:2; 53 of SEQ ID NO: 1 or SEQ ID NO:2; 55 of SEQ ID NO:l or SEQ ID NO:2; 58 of SEQ ID NO:l, SEQ ID NO:2, or SEQ ID NO:3; 59 of SEQ ID NO: 1, SEQ ID NO:2, or SEQ ID NO:3; 60 of SEQ ID NO: 1 or SEQIDNO:2;61 of SEQ ID NO: 1 or SEQ ID NO:2; 62 of SEQ ID NO: 1 or
SEQ ID NO:2; 94 of SEQ ID NO:l, SEQ ID NO:2, or SEQ ID NO:3; 96 of SEQ ID NO: 1, SEQ ID NO:2, or SEQ ID NO:3; 109 of SEQ ID NO: 1, SEQ ID NO:2, or SEQ IDNO:3; 110 of SEQ ID NO: 1 orSEQIDNO:2; 112 of SEQ IDNO:l, SEQ IDNO:2, or SEQIDNO:3; SE 147 ofSEQIDNO:l, SEQIDNO:2, or SEQIDNO:3; 179 of SEQ ID NO:l, SEQ ID NO:2, or SEQ ID NO:3; 180 of SEQIDNO:l or SEQ IDNO:2; 181 ofSEQIDNO:l or SEQ IDNO:2; 183 of SEQ IDNO:l, SEQ ID NO :2, or SEQ ID NO:3; 184 of SEQ ID NO:l, SEQ ID NO:2, or SEQ IDNO:3; 185 ofSEQIDNO:l or SEQ IDNO:2; 186 of SEQ ID NO:l, SEQ IDNO:2, or SEQ IDNO:3; 187 ofSEQIDNO:l or SEQ IDNO:2; 188 of SEQ ID NO: 1 or SEQ ID O:2; 189 of SEQ ID O:l orSEQID O:2;
204 of SEQ ID NO:3; 205 of SEQ ID NO: 1 or SEQ ID NO:2; 247 of SEQ ID NO: 1 or SEQ ID NO:2; 247 of SEQ ID NO:3; 248 of SEQ ID NO: 1 or SEQ ID NO:2; 250 of SEQ ID NO:3; 251 of SEQ ID NO: 1 or SEQ ID NO:2; 264 of SEQ ID NO: 1, SEQ ID NO:2, or SEQ ID NO:3; 265 of SEQ ID NO: 1 or SEQ ID NO:2; and 286 of SEQ ID NO: 1 or SEQ ID NO:2.
[97] In certain further embodiments, the Shiga toxin effector region polypeptides of the invention comprise or consist essentially of a full-length or truncated Shiga toxin A Subunit with at least one substitution within an epitope region, wherein at least one amino acid substitution is to a non-conservative amino acid (see, e.g., Table B, infra) relative to a natively occurring amino acid positioned at one of the following native positions: 1 of SEQ ID NO: 1 or SEQ ID NO:2; 4 of SEQ ID NO:l, SEQ ID NO:2, or SEQ ID NO:3; 8 of SEQ ID NO: 1, SEQ ID NO:2, or SEQ ID NO:3; 9 of SEQ ID NO: 1, SEQ ID NO:2, or SEQIDNO:3; 11 of SEQ ID NO:l, SEQ ID NO:2, or SEQ ID NO:3; 33 of SEQ ID NO: 1 or SEQ ID NO:2; 43 of SEQ ID NO: 1 or SEQ ID NO:2; 45 of SEQ ID NO: 1 or SEQ ID NO:2; 47 of SEQ ID NO: 1 or SEQ ID NO:2; 48 of SEQ ID NO: 1, SEQ ID NO: 2, or SEQ ID NO:3; 49 of SEQ ID NO:l or SEQ ID NO:2; 53 of SEQ ID NO: 1 or SEQ ID NO:2; 55 of SEQ ID NO: 1 or SEQ ID NO:2; 58 of SEQIDNO:l, SEQIDNO:2, orSEQIDNO:3; 59 ofSEQIDNO:l, SEQ ID NO:2, or SEQ ID NO:3; 60 of SEQ ID NO:l or SEQ ID NO:2; 61 of SEQ ID NO: 1 or SEQ ID NO:2; 62 of SEQ ID NO: 1 or SEQ ID NO:2; 94 of SEQ ID NO: 1, SEQ ID NO:2, or SEQ ID NO:3; 96 of SEQ ID NO: 1, SEQ ID NO:2, or SEQIDNO:3; 109 of SEQ ID NO: 1, SEQIDNO:2, or SEQIDNO:3; 110 of SEQ ID NO: 1 or SEQ ID NO:2; 112 of SEQ ID NO: 1, SEQ ID NO:2, or SEQ IDNO:3; SE 147 of SEQ IDNO:l, SEQIDNO:2, orSEQIDNO:3; 179 of SEQ ID NO : 1 , SEQ ID NO :2, or SEQ ID NO : 3 ; 180 of SEQ ID NO : 1 or SEQ IDNO:2; 181 of SEQ IDNO:l or SEQ IDNO:2; 183 ofSEQIDNO:l, SEQ ID NO:2, or SEQ ID NO:3; 184 of SEQ ID NO:l, SEQ ID NO:2, or SEQ ID NO:3; 185 of SEQ ID NO: 1 orSEQIDNO:2; 186 of SEQ ID NO: 1, SEQIDNO:2, or SEQ IDNO:3; 187 of SEQ ID NO: 1 orSEQIDNO:2; 188 of SEQ IDNO:l or SEQ ID NO:2; 189 of SEQ ID NO:l or SEQ ID NO:2; 204 of SEQ ID NO:3;
205 of SEQ ID NO: 1 or SEQ ID NO:2; 247 of SEQ ID NO: 1 or SEQ ID NO:2; 247 of SEQ ID NO:3; 248 of SEQ ID NO: 1 or SEQ ID NO:2; 250 of SEQ ID NO: 3; 251 of SEQ ID NO: 1 or SEQ ID NO:2; 264 of SEQ ID NO: 1, SEQ ID NO:2, or SEQ ID NO:3; 265 of SEQ ID NO: l or SEQ ID NO:2; and 286 of SEQ ID NO: l or SEQ ID NO:2.
[98] In certain further embodiments, the Shiga toxin effector region polypeptides of the invention comprise or consist essentially of a full-length or truncated Shiga toxin A Subunit with at least one amino acid substitution selected from the group consisting of: Kl to A, G, V, L, I, F, M and H; T4 to A, G, V, L, I, F, M, and S; S8 to A, G, V, I, L, F, and M; T9 to A, G, V, I, L, F, M, and S; S9 to A, G, V, L, I, F, and M; Kl 1 to A, G, V, L, I, F, M and H; S33 to A, G, V, L, I, F, and M; S45 to A, G, V, L, I, F, and M; T45 to A, G, V, L, I, F, and M; D47 to A, G, V, L, I, F, S, and Q; N48 to A, G, V, L, and M; L49 to A or G; D53 to A, G, V, L, I, F, S, and Q; R55 to A, G, V, L, I, F, M, Q, S, K, and H; D58 to A, G, V, L, I, F, S, and Q; P59 to A, G, and F; E60 to A, G, V, L, I, F, S, Q, N, D, M, and R; E61 to A, G, V, L, I, F, S, Q, N, D, M, and R; G62 to A; D94 to A, G, V, L, I, F, S, and Q; S96 to A, G, V, I, L, F, and M; S109 to A, G, V, I, L, F, and M; T109 to A, G, V, I, L, F, M, and S; Gl 10 to A; SI 12 to A, G, V, L, I, F, and M; G147 to A; R179 to A, G, V, L, I, F, M, Q, S, K, and H; T180 to A, G, V, L, I, F, M, and S; T181 to A, G, V, L, I, F, M, and S; D183 to A, G, V, L, I, F, S, and Q; D184 to A, G, V, L, I, F, S, and Q; SI 86 to A, G, V, I, L, F, and M; G187 to A; R188 to A, G, V, L, I, F, M, Q, S, K, and H; S189 to A, G, V, I, L, F, and M; R204 to A, G, V, L, I, F, M, Q, S, K, and H; R205 to A, G, V, L, I, F, M, Q, S, K and H; S247 to A, G, V, I, L, F, and M; Y247 to A, G, V, L, I, F, and M; R248 to A, G, V, L, I, F, M, Q, S, K, and H; R250 to A, G, V, L, I, F, M, Q, S, K, and H; R251 to A, G, V, L, I, F, M, Q, S, K, and H; D264 to A, G, V, L, I, F, S, and Q; G264 to A; and T286 to A, G, V, L, I, F, M, and S.
[99] In certain further embodiments, the Shiga toxin effector region polypeptides of the invention comprise or consist essentially of a full-length or truncated Shiga toxin A Subunit with at least one of the following amino acid substitutions KIM, T4I, S8I, T8V, T9I, S9I, K11A, K11H, S33I, S45I, T45I, D47G, N48V, N48F, L49A, D53A, D53G, D53N, R55A, R55V, R55L, D58A, D58F, P59A, P59F, E60I, E60T, E60R, E61A, E61V, E61L, G62A, D94A, S96I, S109V, T109V, G110A, SI 12V, G147A, R179A, T180G, T181I, D183A, D183G, D184A, D184F, L185V, S186A, S186F, G187A, R188A, R188L, S189A, R204A, R205A, S247I, Y247A, R248A, R250A, R251A, D264A, G264A, T286A and/or T286I. These epitope disrupting substitutions may be combined to form a de-immunized Shiga toxin effector polypeptide with multiple substitutions per epitope region and/or multiple epitope regions disrupted while still retaining Shiga toxin effector function. For example, substitutions at the natively positioned residues Kl, T4, S8, T8, T9, S9, Kl 1, Kl 1, S33, S45, T45, D47, N48, L49, D53, R55, D58, P59, E60, E61, G62, D94, S96I, S109, T109, G110, SI 12, G147, R179, T180, T181I, D183, D184, L185, S 186, S186, G187, R188, S 189, R204A, R205, S247, Y247, R248, R250, R251, D264, G264, T286 and/or T286 may be combined, where possible, with substitutions at the natively positioned residues Kl, T4, S8, T8, T9, S9, Kl 1, Kl 1, S33, S45, T45, D47, N48, L49, D53, R55, D58, P59, E60, E61, G62, D94, S96I, S109, T109, G110, SI 12, G147, R179, T180, T181I, D183, D184, L185, S 186, S186, G187, R188, S 189, R204A, R205, S247, Y247, R248, R250, R251, D264, G264, T286 and/or T286 to create de-immunized Shiga toxin effector region polypeptides of the invention.
[100] In other embodiments, the Shiga toxin effector region polypeptides of the invention comprises or consists essentially of a truncated Shiga toxin A Subunit which is shorter than a full-length Shiga toxin A Subunit wherein at least one amino acid is disrupted in a natively positioned epitope region provided in the Examples (Tables 1, 2, 3, 4, and/or 5). Shiga-like toxin 1 A Subunit truncations are catalytically active, capable of enzymatically inactivating ribosomes in vitro, and cytotoxic when expressed within a cell (LaPointe, J Biol Chem 280: 23310- 18 (2005)). The smallest Shiga toxin A Subunit fragment exhibiting full enzymatic activity is a polypeptide composed of residues 1-239 of SltlA (LaPointe, J Biol Chem 280: 23310-18 (2005)). Although the smallest fragment of the Shiga toxin A Subunit reported to retain substantial catalytic activity was residues 75-247 of StxA (Al-Jaufy, Infect Immun 62: 956-60 (1994)), a StxA truncation expressed de novo within a eukaryotic cell requires only up to residue 240 to reach the cytosol and exert catalytic inactivation of ribosomes (LaPointe, J Biol Chem 280: 23310-18 (2005)).
[101] Although de-immunized Shiga toxin effector region polypeptides of the invention may commonly be smaller than the full length A subunit, it is preferred that the de-immunized Shiga toxin effector region maintain the polypeptide region from amino acid position 77 to 239 (SLT-IA (SEQ ID NO: l) or StxA (SEQ ID NO:2)) or the equivalent in other A Subunits of members of the Shiga toxin family (e.g. 77 to 238 of (SEQ ID NO:3)). For example, in certain embodiments of the invention, the Shiga toxin effector region polypeptides derived from SLT-IA may comprise or consist essentially of amino acids 75 to 251 of SEQ ID NO: 1, 1 to 241 of SEQ ID NO: 1, 1 to 251 of SEQ ID NO: 1, or amino acids 1 to 261 of SEQ ID NO: 1 wherein at least one amino acid is disrupted in the natively positioned epitope regions provided in the Examples (Tables 1, 2, 3, 4, and/or 5). Similarly, de-immunized Shiga toxin effector regions derived from StxA may comprise or consist essentially of amino acids 75 to 251 of SEQ ID NO:2, 1 to 241 of SEQ ID NO:2, 1 to 251 of SEQ ID
NO:2, or amino acids 1 to 261 of SEQ ID NO:2 wherein at least one amino acid is disrupted in at least one natively positioned epitope region provided in the Examples (Tables 1, 2, 3, 4, and/or 5). Additionally, the Shiga toxin effector regions derived from SLT-2 may comprise or consist essentially of amino acids 75 to 251 of SEQ ID NO:3, 1 to 241 of SEQ ID NO:3, 1 to 251 of SEQ ID
NO:3, or amino acids 1 to 261 of SEQ ID NO:3 wherein at least one amino acid is disrupted in at least one natively positioned epitope region provided in the Examples (Tables 1, 2, 3, 4, and/or 5).
[102] The invention further provides variants of the polypeptides of the invention, wherein the Shiga toxin effector region differs from a naturally occurring Shiga toxin A Subunit by only or up to 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20, 25, 30, 35, 40 or more amino acid residues (but by no more than that which retains at least 85%, 90%, 95%, 99% or more amino acid sequence identity). Thus, a Shiga toxin effector region polypeptide of the invention derived from an A Subunit of a member of the Shiga toxin family may comprise additions, deletions, truncations, or other alterations from the original sequence so long as at least 85%, 90%, 95%, 99% or more amino acid sequence identity is maintained to a naturally occurring Shiga toxin A Subunit and at least one amino acid is disrupted in at least one natively positioned epitope region provided in the Examples (Tables 1, 2, 3, 4, and/or 5).
[103] Accordingly, in certain embodiments, the Shiga toxin effector region polypeptides comprises or consists essentially of amino acid sequences having at least 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, 97%, 98%, 99%, 99.5% or 99.7% overall sequence identity to a naturally occurring Shiga toxin A Subunit, such as SLT-IA (SEQ ID N0: 1), StxA (SEQ ID N0:2), and/or SLT-2A (SEQ ID NO:3) wherein at least one amino acid is disrupted in at least one natively positioned epitope region provided in the Examples (Tables 1, 2, 3, 4, and/or 5).
[104] Optionally, either a full length or a truncated version of the Shiga toxin A Subunit may comprise one or more mutations (e.g. substitutions, deletions, insertions or inversions) so long as at least one amino acid is disrupted in at least one natively positioned epitope region provided in the Examples (Tables 1, 2, 3, 4, and/or 5). It is preferred in certain embodiments of the invention that the de- immunized Shiga toxin effector region polypeptides have sufficient sequence identity to a naturally occurring Shiga toxin A Subunit to retain cytotoxicity after entry into a cell, either by well-known methods of host cell transformation, trans fection, infection or induction, or by internalization mediated by a cell- targeting binding region linked with the Shiga toxin effector region polypeptide. The most critical residues for enzymatic activity and/or cytotoxicity in the Shiga toxin A Subunits have been mapped to the following residue-positions:
asparagine-75, tyrosine-77, glutamate-167, arginine-170, and arginine-176 among others (Di, Toxicon 57: 535-39 (2011)). In any one of the embodiments of the invention, the de- immunized Shiga toxin effector region polypeptides may preferably but not necessarily maintain one or more conserved amino acids at positions, such as those found at positions 77, 167, 170, and 176 in StxA, SLT- IA, or the equivalent conserved position in other members of the Shiga toxin family which are typically required for cytotoxic activity. The capacity of a cytotoxic protein of the invention to cause cell death, e.g. its cytotoxicity, may be measured using any one or more of a number of assays well known in the art.
B. Proteins Comprising De-Immunized Shiga Toxin Effector Regions
[105] Proteins of the invention comprise a de-immunized Shiga toxin effector region comprising a polypeptide of the invention linked to an extracellular target biomolecule specific binding region. Binding regions of the proteins of the invention comprise one or more polypeptides capable of selectively and specifically binding an extracellular target biomolecule. Binding regions may comprise one or more various polypeptide moieties, such as ligands whether synthetic or naturally occurring ligands and derivatives thereof, immunoglobulin derived domains, synthetically engineered scaffolds as alternatives to immunoglobulin domains, and the like.
[106] There are numerous binding regions known in the art that are useful for targeting polypeptides to specific cell-types via their binding characteristics, such as ligands, monoclonal antibodies, engineered antibody derivatives, and engineered alternatives to antibodies.
[107] According to one specific, but non-limiting aspect, the binding region of the protein of the invention comprises a naturally occurring ligand or derivative thereof that retains binding functionality to an extracellular target biomolecule, commonly a cell surface receptor. For example, various cytokines, growth factors, and hormones known in the art may be used to target the cytotoxic protein to the cell-surface of specific cell types expressing a cognate cytokine receptor, growth factor receptor, or hormone receptor. Certain non-limiting examples of ligands include (alternative names are indicated in parentheses) B- cell activating factors (BAFFs, APRIL), colony stimulating factors (CSFs), epidermal growth factors (EGFs), fibroblast growth factors (FGFs), vascular endothelial growth factors (VEGFs), insulin-like growth factors (IGFs), interferons, interleukins (such as IL-2, IL-6, and IL-23), nerve growth factors (NGFs), platelet derived growth factors, transforming growth factors (TGFs), and tumor necrosis factors (TNFs).
[108] According to certain other embodiments, the binding region comprises a synthetic ligand capable of binding an extracellular target biomolecule. One non-limiting example is antagonists to cytotoxic T-lymphocyte antigen 4 (CTLA-4).
[109] According to one specific, but non-limiting aspect, the binding region may comprise an immunoglobulin-type binding region. The term
"immunoglobulin-type binding region" as used herein refers to a polypeptide region capable of binding one or more target biomolecules, such as an antigen or epitope. Binding regions may be functionally defined by their ability to bind to target molecules. Immunoglobulin-type binding regions are commonly derived from antibody or antibody-like structures; however, alternative scaffolds from other sources are contemplated within the scope of the term.
[110] Immunoglobulin (Ig) proteins have a structural domain known as an Ig domain. Ig domains range in length from about 70-110 amino acid residues and possess a characteristic Ig-fold, in which typically 7 to 9 antiparallel beta strands arrange into two beta sheets which form a sandwich-like structure. The Ig fold is stabilized by hydrophobic amino acid interactions on inner surfaces of the sandwich and highly conserved disulfide bonds between cysteine residues in the strands. Ig domains may be variable (IgV or V-set), constant (IgC or C-set) or intermediate (Igl or I-set). Some Ig domains may be associated with a complementarity determining region (CDR) which is important for the specificity of antibodies binding to their epitopes. Ig-like domains are also found in non-immunoglobulin proteins and are classified on that basis as members of the Ig superfamily of proteins. The HUGO Gene Nomenclature
Committee (HGNC) provides a list of members of the Ig-like domain containing family.
[I l l] An immunoglobulin-type binding region may be a polypeptide sequence of an antibody or antigen-binding fragment thereof wherein the amino acid sequence has been varied from that of a native antibody or an Ig-like domain of a non-immunoglobulin protein, for example by molecular engineering or selection by library screening. Because of the relevance of recombinant DNA techniques and in vitro library screening in the generation of immunoglobulin-type binding regions, antibodies can be redesigned to obtain desired characteristics, such as smaller size, cell entry, or other therapeutic improvements. The possible variations are many and may range from the changing of just one amino acid to the complete redesign of, for example, a variable region. Typically, changes in the variable region will be made in order to improve the antigen-binding characteristics, improve variable region stability, or reduce the potential for immunogenic responses.
[112] There are numerous immunoglobulin-type binding regions contemplated as components of the present invention. In certain embodiments, the immunoglobulin-type binding region is derived from an immunoglobulin binding region, such as an antibody paratope capable of binding an extracellular target biomolecule. In certain other embodiments, the immunoglobulin-type binding region comprises an engineered polypeptide not derived from any immunoglobulin domain but which functions like an immunoglobulin binding region by providing high-affinity binding to an extracellular target biomolecule. This engineered polypeptide may optionally include polypeptide scaffolds comprising or consisting essentially of complementary determining regions from immunoglobulins as described herein.
[113] There are also numerous binding regions in the prior art that are useful for targeting polypeptides to specific cell-types via their high-affinity binding characteristics. In certain embodiments, the binding region of the present proteins is selected from the group which includes single-domain antibody domains (sdAbs), nanobodies, heavy-chain antibody domains derived from camelids (VHH fragments), bivalent nanobodies, heavy-chain antibody domains derived from cartilaginous fishes, immunoglobulin new antigen receptors (IgNARs), VNAR fragments, single-chain variable (scFv) fragments,
multimerizing scFv fragments (diabodies, triabodies, tetrabodies), bispecific tandem scFv fragments, disulfide stabilized antibody variable (Fv) fragments, disulfide stabilized antigen-binding (Fab) fragments consisting of the VL, VH, CL and CH 1 domains, divalent F(ab')2 fragments, Fd fragments consisting of the heavy chain and CHI domains, single chain FV-CH3 minibodies, bispecific minibodies, dimeric CH2 domain fragments (CH2D), FC antigen binding domains (Fcabs), isolated complementary determining region 3 (CDR3) fragments, constrained framework region 3, CDR3, framework region 4 (FR3-CDR3-FR4) polypeptides, small modular immunopharmaceutical (SMIP) domains, and any genetically manipulated counterparts of the foregoing that retain its paratope and binding function (see Saerens D et al, Curr. Opin. Pharmacol 8: 600-8 (2008); Dimitrov D, MAbs 1 : 26-8 (2009); Weiner L, Cell 148: 1081-4 (2012); Ahmad Z et al, Clin Dev Immunol 2012: 980250 (2012)).
[114] In accordance with certain other embodiments, the binding region includes engineered, alternative scaffolds to immunoglobulin domains that exhibit similar functional characteristics, such as high-affinity and specific binding of target biomolecules, and enables the engineering of improved characteristics, such as greater stability or reduced immunogenicity. For certain embodiments of the proteins of the invention, the binding region is selected from the group which includes engineered, fibronection-derived, 10th fibronectin type III (10Fn3) domain (monobodies, AdNectins™, or AdNexins™); engineered, tenacs in-derived, tenacsin type III domain (Centryns™); engineered, ankyrin repeat motif containing polypeptide (DARPins™); engineered, low-density- lipoprotein-receptor-derived, A domain (LDLR-A) (Avimers™); lipocalin (anticalins); engineered, protease inhibitor-derived, Kunitz domain; engineered, Protein-A-derived, Z domain (Affibodies™); engineered, gamma-B crystalline- derived scaffold or engineered, ubiquitin-derived scaffold (Affilins); Sac7d- derived polypeptides (Nanoffitins® or affitins); engineered, Fyn-derived, SH2 domain (Fynomers®); miniproteins; C-type lectin-like domain scaffolds;
engineered antibody mimics; and any genetically manipulated counterparts of the foregoing that retains its binding functionality (W5rn A, Pluckthun A, JMol Biol 305: 989-1010 (2001); Xu L et al, Chem Biol 9: 933-42 (2002); Wikman M et al, Protein Eng Des Sel 17: 455-62 (2004); Binz H et al, Nat Biotechnol 23: 1257-68 (2005); Hey T et al, Trends Biotechnol 23 :514-522 (2005); Holliger P, Hudson P, Nat Biotechnol 23: 1 126-36 (2005); Gill D, Damle N, Curr Opin Biotech 17: 653-8 (2006); Koide A, Koide S, Methods Mol Biol 352: 95-109 (2007); Byla P et al, J Biol Chem 285: 12096 (2010); Zoller F et al, Molecules 16: 2467-85 (2011)).
[115] Any of the above binding regions may be used as a component of the present invention so long as the binding region component has a dissociation constant of 10"5 to 10"12 moles per liter, preferably less than 200 nanomolar (nM), towards an extracellular target biomolecule. Extracellular Target Biomolecules
[116] The binding region of the protein of the invention comprises a polypeptide region capable of binding specifically to an extracellular target biomolecule, preferably which is physically-coupled to the surface of a cell type of interest, such as a cancer cell, tumor cell, plasma cell, infected cell, or host cell harboring an intracellular pathogen.
[117] The term "target biomolecule" refers to a biological molecule, commonly a protein or a protein modified by post-translational modifications, such as glycosylation, which is capable of being bound by a binding region to target a protein to a specific cell-type or location within an organism. Extracellular target biomolecules may include various epitopes, including unmodified polypeptides, polypeptides modified by the addition of biochemical functional groups, and glycolipids (see e.g. U.S. Patent 5,091, 178; EP 2431743). It is desirable that an extracellular target biomolecule be endogenously internalized or be readily forced to internalize upon interaction with a protein of the invention.
[118] For purposes of the present invention, the term "extracellular" with regard to modifying a target biomolecule refers to a biomolecule that has at least a portion of its structure exposed to the extracellular environment. Extracellular target biomolecules include cell membrane components, transmembrane spanning proteins, cell membrane-anchored biomolecules, cell-surface-bound biomolecules, and secreted biomolecules.
[119] With regard to the present invention, the phrase "physically coupled" when used to describe a target biomolecule means both covalent and/or non- covalent intermolecular interactions that couple the target biomolecule, or a portion thereof, to the outside of a cell, such as a plurality of non-covalent interactions between the target biomolecule and the cell where the energy of each single interaction is on the order of about 1-5 kiloCalories (e.g. electrostatic bonds, hydrogen bonds, Van der Walls interactions, hydrophobic forces, etc.). All integral membrane proteins can be found physically coupled to a cell membrane, as well as peripheral membrane proteins. For example, an extracellular target biomolecule might comprise a transmembrane spanning region, a lipid anchor, a glycolipid anchor, and/or be non-covalently associated (e.g. via non-specific hydrophobic interactions and/or lipid binding interactions) with a factor comprising any one of the foregoing.
[120] The binding regions of the proteins of the invention may be designed or selected based on numerous criteria, such as the cell-type specific expression of their target biomolecules and/or the physical localization of their target biomolecules with regard to specific cell types. For example, certain proteins of the present invention comprise binding domains capable of binding cell-surface targets which are expressed exclusively by only one cell-type to the cell surface. This permits the targeted cell-killing of specific cell types with a high preferentiality (at least a 3 -fold cytotoxic effect) over "bystander" cell types that do not express the extracellular target biomolecule. Alternatively, the expression of the target biomolecule of the binding region may be non-exclusive to one cell type if the extracellular target biomolecule is expressed in low enough amounts and/or physically coupled in low amounts with cell types that are not to be targeted. This also permits the targeted cell-killing of specific cell types with a high preferentiality (at least a 3 -fold cytotoxic effect) over "bystander" cell types that do not express significant amounts of the extracellular target biomolecule or are not physically coupled to significant amounts of the extracellular target biomolecule. A targeted cell may be killed using the cytotoxic proteins of the invention under varied conditions of the cell, such as ex vivo, in vitro cultured, or in vivo— including cells in situ in their native locations within a multicellular organism.
[121] Extracellular target biomolecules of the binding region of the proteins of the invention may include biomarkers over-proportionately or exclusively present on cancer cells, immune cells, and cells infected with intracellular pathogens, such as viruses, bacteria, fungi, prions, or protozoans.
De-Immunized Shiga Toxin Effector Regions
[122] In certain embodiments of the proteins of the invention, one or more amino acid residues may be mutated, inserted, or deleted in order to increase the enzymatic activity of the de-immunized Shiga toxin effector region. For example, mutating residue-position alanine-231 in StxlA to glutamate increased its enzymatic activity in vitro (Suhan M, Hovde C, Infect Immun 66: 5252-9 (1998)).
[123] In certain embodiments of the proteins of the invention, one or more amino acid residues may be mutated or deleted in order to reduce or eliminate catalytic and/or cytotoxic activity of the de-immunized Shiga toxin effector region. The catalytic and/or cytotoxic activity of the A Subunits of members of the Shiga toxin family may be diminished or eliminated by mutation or truncation as long as at least one amino acid is disrupted in at least one natively positioned epitope region provided in the Examples (Tables 1, 2, 3, 4, and/or 5). The positions labeled tyrosine-77, glutamate- 167, arginine-170, tyrosine-114, and tryptophan-203 have been shown to be important for the catalytic activity of Stx, Stxl, and Stx2 (Hovde C et al, Proc Natl Acad Sci USA 85: 2568-72 (1988); Deresiewicz R et al, Biochemistry 31 : 3272-80 (1992); Deresiewicz R et al, Mol Gen Genet 241 : 467-73 (1993); Ohmura M et al, Microb Pathog 15: 169-76 (1993); Cao C et al., Microbiol Immunol ^: 441-7 (1994); Suhan, Infect Immun 66: 5252-9 (1998)). Mutating both glutamate-167 and arginine-170 eliminated the enzymatic activity of Slt-I Al in a cell-free ribosome inactivation assay (LaPointe, J Biol Chem 280: 23310-18 (2005)). In another approach using de novo expression of Slt-I Al in the endoplasmic reticulum, mutating both glutamate-167 and arginine-170 or truncating SLt-I Al to residues 1-239 eliminated Slt-I Al fragment cytotoxicity at that expression level (LaPointe, J Biol Chem 280: 23310-18 (2005)).
[124] The proteins of the invention each comprise a de-immunized Shiga toxin effector region polypeptide which retains at least one Shiga toxin effector function but which may be engineered from a cytotoxic parental molecule to a protein with diminished or abolished cytotoxicity for non-cytotoxic functions, e.g., effectuating cytostasis, delivery of exogenous materials, and/or detection of cell types, by mutating one or more key residues for enzymatic activity. This general structure is modular in that the polypeptides of the invention may be linked to any number of diverse compositions of matter, such as binding regions and/or detection promoting agents for various applications as described herein.
[125] The immunogenicity of a molecule (the ability to induce an antibody and/or cell-mediated immune response) can be assessed by observing any immune response (antibody and/or immune cell-mediated) to the molecule after administration to a living organism, such as a chordate. Certain immune responses can be measured, such as the amount and formation of antibodies specifically targeting the administered molecule over time. The presence of antibodies which specifically bind the administered molecule indicate 1) the pre- existence of one or more antibodies which recognized the administered molecule and/or 2) the induction of the de novo formation of one or more antibodies which recognize the administered molecule.
[126] The existence of pre-formed anti-molecule antibodies can be determined by investigating pre-administration serum for the presence of anti- molecule antibodies. The induction of de novo anti-"administered molecule" antibody formation can be determined by monitoring post-administration serum for the amount of anti-molecule antibodies generated over time.
[127] The amount of antibodies induced in chordates after the administration of a molecule (e.g. Shiga toxin effector region polypeptide) can be measured by comparing the amount of pre-administration, anti-molecule antibodies to the amount of post-administration, anti-molecule antibodies. The amount of anti- "administered molecule" antibodies induced in a chordate after administration is indicative of the general immunogenicity of the molecule and the molecule's ability to induce various immune responses in various chordates, such as inducing increased and diversified anti-molecule antibody production after administration, immune cell-mediated immune responses, molecule neutralizing activities, hypersensitivity reactions, anaphylaxis, anaphylactoid reactions, and other immune responses.
[128] It may be difficult to gauge the immunogenicity of a weakly
immunogenic molecule without a reference point, such as another more immunogenic molecule. The relative immunogenicity of two molecules (e.g. a wild-type Shiga toxin effector region polypeptide and a de-immunized Shiga toxin effector polypeptide) can be assessed by observing the relative differences in anti-molecule antibodies produced for each molecule respectively after administration of each molecule individually to different organisms. The relative induction of de novo anti-"administered molecule" antibody formation can be determined by measuring the relative differences in post-administration sera for the amount of anti- molecule antibodies generated over time, for each molecule respectively.
[129] The amount of antibodies induced in a chordate, such as a mouse, treated with different molecules (e.g. a wild-type Shiga toxin effector region polypeptide and a de-immunized Shiga toxin effector polypeptide) can be measured with standard ELISA-based assays and used to compare the relative immunogenicity of the different molecules.
Endoplasmic Reticulum Retention/Retrieval Signal Motif of a Member of the KDEL Family
[130] For purposes of the present invention, the phrase "endoplasmic reticulum retention/retrieval signal motif," KDEL-type signal motif, or signal motif refers to any member of the KDEL family capable of functioning within a eukaryotic cell to promote subcellular localization of a protein to the endoplasmic reticulum via KDEL receptors.
[131] The carboxy -terminal lysine-asparagine-glutamate-leucine (KDEL) sequence is a canonical, endoplasmic reticulum retention and retrieval signal motif for soluble proteins in eukaryotic cells and is recognized by the KDEL receptors (see, Capitani M, Sallese M, FEBS Lett 583: 3863-71 (2009), or review). The KDEL family of signal motifs includes many KDEL-like motifs, such as HDEL, RDEL, WDEL, YDEL, HEEL, KEEL, REEL, KFEL, KIEL, DKEL, KKEL, HNEL, HTEL, KTEL, and HVEL, all of which are found at the carboxy -terminals of proteins which are known to be residents of the lumen of the endoplasmic reticulum of throughout multiple phylogenetic kingdoms
(Munro S, Pelham H, C¾// 48: 899-907 (1987); Raykhel I et al, J Cell Biol 179: 1193-204 (2007)). The KDEL signal motif family includes at least 46 polypeptide variants shown using synthetic constructs (Raykhel, J Cell Biol 179: 1193-204 (2007)). Additional KDEL signal motifs include ALEDEL,
HAEDEL, HLEDEL, KLEDEL, IRSDEL, ERSTEL, and RPSTEL (Alanen H et al, JMol Biol 409: 291-7 (2011)). A generalized consensus motif representing the majority of KDEL signal motifs has been described as [KRHQSA]-[DENQ]- E-L (Hulo N et al, Nucleic Acids Res 34: D227-30 (2006)).
[132] Proteins containing KDEL family signal motifs are bound by KDEL receptors distributed throughout the Golgi complex and transported to the endoplasmic reticulum by a microtubule-dependent mechanism for release into the lumen of the endoplasmic reticulum (Griffiths G et al, J Cell Biol 127: 1557- 74 (1994); Miesenb5ck G, Rothman J, J Cell Biol 129: 309-19 (1995)). KDEL receptors dynamically cycle between the Golgi complex and endoplasmic reticulum (Jackson M et al, EMBO J. 9: 3153-62 (1990); Schutze M et al, EMBO J. 13: 1696-1705 (1994)).
[133] For purposes of the present invention, the members of the KDEL family include synthetic signal motifs able to function within a eukaryotic cell to promote subcellular localization of a protein to the endoplasmic reticulum via KDEL receptors. In other words, some members of the KDEL family might not occur in nature or have yet to be observed in nature but have or may be constructed and empirically verified using methods known in the art; see e.g., Raykhel I et al, J Cell Biol 179: 1193-204 (2007).
[134] As a component of certain embodiments of the proteins of the invention, the KDEL-type signal motif is physically located, oriented, or arranged within the protein such that it is on a carboxy -terminal.
[135] For the purposes of the present invention, the specific order or orientation is not fixed for the Shiga toxin effector region and the binding region in relation to each other or the entire protein's N-terminal(s) and C-terminal(s) (see e.g. Figure 1). In the proteins of the invention, the binding regions and Shiga toxin effector regions may be directly linked to each other and/or suitably linked to each other via one or more intervening polypeptide sequences, such as with one or more linkers well known in the art. Optionally, a protein of the invention may further comprise a carboxy-terminal endoplasmic retention/retrieval signal motif, such as KDEL.
[136] The general structure of the proteins of the present invention is modular, in that various, diverse binding regions may be used with the same de- immunized Shiga toxin effector region to provide for diverse targeting of various extracellular target biomolecules and thus targeting of cytotoxicity, cytostasis, and/or exogenous material delivery to various diverse cell types. De-immunized Shiga toxin effector regions which are not cytotoxic due to improper subcellular routing may still be useful for delivering exogenous materials into cells. II. Linkages Connecting Polypeptide Components of the Invention and/or their Subcomponents
[137] Individual polypeptide and/or protein components of the invention, e.g., the binding regions and Shiga toxin effector regions (which may be cytotoxic and/or harbor one or more mutations altering, reducing or eliminating catalytic activity and/or cytotoxicity), may be suitably linked to each other via one or more linkers well known in the art and/or described herein. Individual polypeptide subcomponents of the binding regions, e.g. heavy chain variable regions (VH), light chain variable regions (VL), CDR, and/or ABR regions, may be suitably linked to each other via one or more linkers well known in the art and/or described herein (see e.g. Weisser N, Hall J, Biotechnol Adv 27: 502-20 (2009); Chen X et al, Adv Drug Deliv Rev 65: 1357-69 (2013)). Protein components of the invention, e.g., multi-chain binding regions, may be suitably linked to each other or other polypeptide components of the invention via one or more linkers well known in the art. Peptide components of the invention, e.g., KDEL family endoplasmic reticulum retention/retrieval signal motifs, may be suitably linked to another component of the invention via one or more linkers, such as a proteinaceous linker, which are well known in the art.
[138] Suitable linkers are generally those which allow each polypeptide component of the invention to fold with a three-dimensional structure very similar to the polypeptide components produced individually without any linker or other component. Suitable linkers include single amino acids, peptides, polypeptides, and linkers lacking any of the aforementioned such as various non- proteinaceous carbon chains, whether branched or cyclic (see e.g. Chen X et al, Adv Drug Deliv Rev 65: 1357-69 (2013)).
[139] Suitable linkers may be proteinaceous and comprise one or more amino acids, peptides, and/or polypeptides. Proteinaceous linkers are suitable for both recombinant fusion proteins and chemically linked conjugates. A proteinaceous linker typically has from about 2 to about 50 amino acid residues, such as, e.g., from about 5 to about 30 or from about 6 to about 25 amino acid residues. The length of the linker selected will depend upon a variety of factors, such as, e.g., the desired property or properties for which the linker is being selected (see e.g. Chen X et al, Adv Drug Deliv Rev 65: 1357-69 (2013)).
[140] Suitable linkers may be non-proteinaceous, such as, e.g. chemical linkers (see e.g. Dosio F et al, Toxins 3: 848-83 (201 1); Feld J et al, Oncotarget 4: 397- 412 (2013)). Various non-proteinaceous linkers known in the art may be used to link binding regions to the Shiga toxin effector regions, such as linkers commonly used to conjugate immunoglobulin-derived polypeptides to heterologous polypeptides. For example, polypeptide regions may be linked using the functional side chains of their amino acid residues and carbohydrate moieties such as, e.g., a carboxy, amine, sulfhydryl, carboxylic acid, carbonyl, hydroxyl, and/or cyclic ring group. For example, disulfide bonds and thioether bonds may be used to link two or more polypeptides (see e.g. Fitzgerald D et al, Bioconjugate Chem 1 : 264-8 (1990); Pasqualucci L et al, Haematologica 80: 546-56 (1995)). In addition, non-natural amino acid residues may be used with other functional side chains, such as ketone groups (see e.g. Sun S et al, Chembiochem Jul 18 (2014); Tian F et al, Proc Natl Acad Sci USA 11 1 : 1766- 71 (2014)). Examples of non-proteinaceous chemical linkers include but are not limited to N-succinimidyl (4-iodoacetyl)-aminobenzoate, ^-(N-succinimidyl) thioacetate (SATA), N-succinimidyl-oxycarbonyl-cu-methyl-a-(2-pyridyldithio) toluene (SMPT), N-succinimidyl 4-(2-pyridyldithio)-pentanoate (SPP), succinimidyl 4-(N-maleimidomethyl) cyclohexane carboxylate (SMCC or MCC), sulfosuccinimidyl (4-iodoacetyl)-aminobenzoate, 4-succinimidyl- oxycarbonyl-a-(2-pyridyldithio) toluene, sulfosuccinimidyl-6-(a-methyl-a- (pyridyldithiol)-toluamido) hexanoate, N-succinimidyl-3-(-2-pyridyldithio)- proprionate (SPDP), succinimidyl 6(3(-(-2-pyridyldithio)-proprionamido) hexanoate, sulfosuccinimidyl 6(3(-(-2-pyridyldithio)-propionamido) hexanoate, maleimidocaproyl (MC), maleimidocaproyl-valine-citrulline-p- aminobenzyloxycarbonyl (MC-vc-PAB), 3-maleimidobenzoic acid N- hydroxysuccinimide ester (MBS), alpha-alkyl derivatives, sulfoNHS-ATMBA (sulfosuccinimidyl N-[3-(acetylthio)-3-methylbutyryl-beta-alanine]), sulfodicholorphenol, 2-iminothiolane, 3-(2-pyridyldithio)-propionyl hydrazide, Ellman's reagent, dichlorotriazinic acid, and S-(2-thiopyridyl)-L-cysteine (see e.g. Thorpe P et al, Eur J Biochem 147: 197-206 (1985); Thorpe P et al, Cancer Res 47: 5924-31 (1987); Thorpe P et al, Cancer Res 48: 6396-403 (1988); Grossbard M et al., Blood 79: 576-85 (1992); Lui C et al, Proc Natl Acad Sci USA 93: 8618-23 (1996); Doronina S et al, Nat Biotechnol 21: 778-84 (2003); Feld J et al, Oncotarget 4: 397-412 (2013)).
[141] Suitable linkers, whether proteinaceous or non-proteinaceous, may include, e.g., protease sensitive, environmental redox potential sensitive, pH sensitive, acid cleavable, photocleavable, and/or heat sensitive linkers (see e.g. Dosio F et al, Toxins 3 : 848-83 (2011); Chen X et al., Adv Drug Deliv Rev 65: 1357-69 (2013); Feld J et al, Oncotarget 4: 397-412 (2013)).
[142] Proteinaceous linkers may be chosen for incorporation into recombinant fusion proteins of the invention. For recombinant fusion proteins of the invention, linkers typically comprise about 2 to 50 amino acid residues, preferably about 5 to 30 amino acid residues (Argos P, JMol Biol 211: 943-58 (1990); Williamson M, Biochem J 297: 240-60 (1994); George R, Heringa J, Protein Eng 15: 871-9 (2002); Kreitman R, AAPSJ S: E532-51 (2006)).
Commonly, proteinaceous linkers comprise a majority of amino acid residues with polar, uncharged, and/or charged residues, such as, e.g., threonine, proline, glutamine, glycine, and alanine (see e.g. Huston J et al. Proc Natl Acad Sci U.S.A. 85: 5879-83 (1988); Pastan I et al, Annu Rev Med 58: 221-37 (2007); Li J et al, Cell Immunol 118: 85-99 (1989); Cumber A et al. Bioconj Chem 3: 397- 401 (1992); Friedman P et al, Cancer Res 53: 334-9 (1993); Whitlow M et al, Protein Engineering 6: 989-95 (1993); Siegall C et al, J Immunol 152: 2377-84 (1994); Newton et al. Biochemistry 35: 545-53 (1996); Ladurner et al. J Mol Biol 273: 330-7 (1997); Kreitman R et al., Leuk Lymphoma 52: 82-6 (2011); U.S. 4,894,443). Non-limiting examples of proteinaceous linkers include alanine-serine-glycine-glycine-proline-glutamate (ASGGPE), valine-methionine (VM), alanine- methionine (AM), AM(G2 to 4S)XAM where G is glycine, S is serine, and x is an integer from 1 to 10.
[143] Proteinaceous linkers may be selected based upon the properties desired. Proteinaceous linkers may be chosen by the skilled worker with specific features in mind, such as to optimize one or more of the fusion molecule's folding, stability, expression, solubility, pharmacokinetic properties, pharmacodynamic properties, and/or the activity of the fused domains in the context of a fusion construct as compared to the activity of the same domain by itself. For example, proteinaceous linkers may be selected based on flexibility, rigidity, and/or cleavability (see e.g. Chen X et al, Adv Drug Deliv Rev 65: 1357-69 (2013)). The skilled worker may use databases and linker design software tools when choosing linkers. Certain linkers may be chosen to optimize expression (see e.g. Turner D et al, Jlmmunl Methods 205: 43-54 (1997)). Certain linkers may be chosen to promote intermolecular interactions between identical polypeptides or proteins to form homomultimers or different polypeptides or proteins to form heteromultimers. For example, proteinaceous linkers may be selected which allow for desired non-covalent interactions between polypeptide components of the proteins of the invention, such as, e.g., interactions related to the formation dimers and other higher order multimers (see e.g. U.S. 4,946,778).
[144] Flexible proteinaceous linkers are often greater than 12 amino acid residues long and rich in small, non-polar amino acid residues, polar amino acid residues, and/or hydrophilic amino acid residues, such as, e.g., glycines, serines, and threonines (see e.g. Bird R et al, Science 242: 423-6 (1988); Friedman P et al, Cancer Res 53: 334-9 (1993); Siegall C et al, J Immunol 152: 2377-84 (1994)). Flexible proteinaceous linkers may be chosen to increase the spatial separation between components and/or to allow for intramolecular interactions between components. For example, various "GS" linkers are known to the skilled worker and are composed of multiple glycines and/or one or more serines, sometimes in repeating units, such as, e.g., (GxS)n, (SxG)n, (GGGGS)n, and (G)n. in which x is 1 to 6 and n is 1 to 30 (see e.g. WO 96/06641). Non- limiting examples of flexible proteinaceous linkers include GKSSGSGSESKS, GSTSGSGKSSEGKG, GSTSGSGKSSEGSGSTKG, GSTSGSGKSSEGKG, GSTSGSGKPGSGEGSTKG, EGKSSGSGSESKEF, SRSSG, and SGSSC.
[145] Rigid proteinaceous linkers are often stiff alpha-helical structures and rich in proline residues and/or one or more strategically placed prolines (see Chen X et al, Adv Drug Deliv Rev 65: 1357-69 (2013)). Rigid linkers may be chosen to prevent intramolecular interactions between linked components.
[146] Suitable linkers may be chosen to allow for in vivo separation of components, such as, e.g., due to cleavage and/or environment-specific instability (see Dosio F et al, Toxins 3: 848-83 (2011); Chen X et al, Adv Drug Deliv Rev 65: 1357-69 (2013)). In vivo cleavable proteinaceous linkers are capable of unlinking by proteolytic processing and/or reducing environments often at a specific site within an organism or inside a certain cell type (see e.g. Doronina S et al, Bioconjug Chem 17: 144-24 (2006); Erickson H et al, Cancer Res 66: 4426-33 (2006)). In vivo cleavable proteinaceous linkers often comprise protease sensitive motifs and/or disulfide bonds formed by one or more cysteine pairs (see e.g. Pietersz G et al., Cancer Res 48: 4469-76 (1998); The J et al, J Immunol Methods 1 10: 101-9 (1998); see Chen X et al, Adv Drug Deliv Rev 65: 1357-69 (2013)). In vivo cleavable proteinaceous linkers can be designed to be sensitive to proteases that exist only at certain locations in an organism, compartments within a cell, and/or become active only under certain physiological or pathological conditions (such as, e.g., proteases with abnormally high levels, proteases overexpressed at certain disease sites, and proteases specifically expressed by a pathogenic microorganism). For example, there are proteinaceous linkers known in the art which are cleaved by proteases present only intracellularly, proteases present only within specific cell types, and proteases present only under pathological conditions like cancer or
inflammation, such as, e.g., R-x-x-R motif and
AMGRSGGGCAGNRVGSSLSCGGLNLQAM.
[147] In certain embodiments of the proteins of the invention, a linker may be used which comprises one or more protease sensitive sites to provide for cleavage by a protease present within a target cell. In certain embodiments of the proteins of the invention, a linker may be used which is not cleavable to reduce unwanted toxicity after administration to a vertebrate organism. [148] Suitable linkers may include, e.g., protease sensitive, environmental redox potential sensitive, pH sensitive, acid cleavable, photocleavable, and/or heat sensitive linkers, whether proteinaceous or non-proteinaceous (see Chen X et al, Adv Drug Deliv Rev 65: 1357-69 (2013)).
[149] Suitable cleavable linkers may include linkers comprising cleavable groups which are known in the art such as, e.g., Zarling D et al, J Immunol 124: 913-20 (1980); Jung S, Moroi M, Biochem Biophys Acta 761 : 152-62 (1983); Bouizar Z et al, Eur J Biochem 155: 141-7 (1986); Park L et al, J Biol Chem 261: 205-10 (1986); Browning J, Ribolini A, J Immunol 143: 1859-67 (1989); Joshi S, Burrows R, J Biol Chem 265: 14518-25 (1990)).
[150] Suitable linkers may include pH sensitive linkers. For example, certain suitable linkers may be chosen for their instability in lower pH environments to provide for dissociation inside a subcellular compartment of a target cell. For example, linkers that comprise one or more trityl groups, derivatized trityl groups, bismaleimideothoxy propane groups, adipic acid dihydrazide groups, and/or acid labile transferrin groups, may provide for release of components of the proteins of the invention, e.g. a polypeptide component, in environments with specific pH ranges (see e.g. Welh5ner H et al, J Biol Chem 266: 4309-14 (1991); Fattom A et al, Infect Immun 60: 584-9 (1992)). Certain linkers may be chosen which are cleaved in pH ranges corresponding to physiological pH differences between tissues, such as, e.g., the pH of tumor tissue is lower than in healthy tissues (see e.g. U.S. 5,612,474).
[151] Photocleavable linkers are linkers that are cleaved upon exposure to electromagnetic radiation of certain wavelength ranges, such as light in the visible range (see e.g. Goldmacher V et al, Bioconj Chem 3: 104-7 (1992)). Photocleavable linkers may be used to release a component of a protein of the invention, e.g. a polypeptide component, upon exposure to light of certain wavelengths. Non-limiting examples of photocleavable linkers include a nitrobenzyl group as a photocleavable protective group for cysteine,
nitrobenzyloxycarbonyl chloride cross-linkers, hydroxypropylmethacrylamide copolymer, glycine copolymer, fluorescein copolymer, and methylrhodamine copolymer (Hazum E et al, Pept Proc Eur Pept Symp, 16th, Brunfeldt K, ed., 105-110 (1981); Senter et al, Photochem Photobiol 42: 231-7 (1985); Yen et al, Makromol Chem 190: 69-82 (1989); Goldmacher V et al, Bioconj Chem 3: 104- 7 (1992)). Photocleavable linkers may have particular uses in linking components to form proteins of the invention designed for treating diseases, disorders, and conditions that can be exposed to light using fiber optics.
[152] In certain embodiments of the proteins of the invention, a binding region is linked to a Shiga toxin effector region using any number of means known to the skilled worker, including both covalent and noncovalent linkages (see e.g. Chen X et al, Adv Drug Deliv Rev 65: 1357-69 (2013); Behrens C, Liu B, MAbs 6: 46-53 (2014).
[153] In certain embodiments of the proteins of the invention, the protein comprises a binding region which is a scFv with a linker connecting a heavy chain variable (VH) domain and a light chain variable (VL) domain. There are numerous linkers known in the art suitable for this purpose, such as, e.g., the 15- residue (Gly4Ser)3 peptide. Suitable scFv linkers which may be used in forming non-covalent multivalent structures include GGS, GGGS, GGGGS,
GGGGSGGG, GGSGGGG, GSTSGGGSGGGSGGGGSS, and
GSTSGSGKPGSSEGSTKG (Pluckthun A, Pack P, Immunotechnology 3: 83- 105 (1997); Atwell J et al, Protein Eng 12: 597-604 (1999); Wu A et al, Protein Eng 14: 1025-33 (2001); Yazaki P et al, J Immunol Methods 253 : 195- 208 (2001); Carmichael J et al, JMol Biol 326: 341-51 (2003); Arndt M et al, FEBS Lett 578: 257-61 (2004); Bie C et al, World J Hepatol 2: 185-91 (2010)).
[154] Suitable methods for linkage of the components of the proteins of the invention may be by any method presently known in the art for accomplishing such, so long as the attachment does not substantially impede the binding capability of the binding regions, the cellular internalization of the protein, and/or desired toxin effector functions of the Shiga toxin effector region as measured by an appropriate assay, including assays described herein.
[155] For the purposes of the present invention, the specific order or orientation is not fixed for the Shiga toxin effector region and the cell-targeting binding region in relation to each other or the entire protein (see e.g. Figure 1). The components of the polypeptides and proteins of the invention may be arranged in any order provided that the desired activities of the binding region and the Shiga toxin effector region are not eliminated. In the above embodiments of polypeptides and proteins of the invention, the binding regions, Shiga toxin effector regions (which may be cytotoxic and/or harbor one or more mutations reducing or eliminating catalytic activity and/or cytotoxicity), and endoplasmic reticulum retention/retrieval signal motif may be directly linked to each other and/or suitably linked to each other via one or more intervening polypeptide sequences, such as with one or more linkers well known in the art and/or described herein.
III. Examples of Specific Structural Variations of the De-Immunized Shiga Toxin Effector Region Polypeptides and Proteins
[156] To create a de-immunized Shiga toxin effector polypeptide, in principle any amino acid in the provided epitope regions may be disrupted by various means, such as, e.g., deletion, insertion, inversion, rearrangement, substitution, and chemical modification of side chains. However, disrupting certain amino acids and polypeptide regions using certain disruptions are more likely to successfully reduce antigenicity and/or immunogenicity while retaining a Shiga toxin effector function. For example, terminal truncations and internal amino acid substitutions are preferred because they maintain the overall amino acid spacing of the Shiga toxin effector region and thus are more likely to maintain Shiga toxin effector functions.
[157] Among certain embodiments of the present invention, the polypeptides comprise the de-immunized Shiga toxin effector region comprising or consisting essentially of amino acids 75 to 251 of SLT-1A (SEQ ID O: l), StxA (SEQ ID NO: 2), and/or SLT-2A (SEQ ID NO:3) wherein at least one amino acid is disrupted in the natively positioned epitope regions provided in the Examples (Tables 1, 2, 3, 4, and/or 5). Among certain other embodiments are polypeptides comprising a de-immunized Shiga toxin effector region derived from amino acids 1 to 241 of SLT-1A (SEQ ID NO: l), StxA (SEQ ID NO:2), and/or SLT- 2A (SEQ ID NO:3) wherein at least one amino acid is disrupted in the natively positioned epitope regions provided in the Examples (Tables 1, 2, 3, 4, and/or 5). Further embodiments are polypeptides comprising a de-immunized Shiga toxin effector region which is derived from amino acids 1 to 251 of SLT-1A (SEQ ID NO: 1), StxA (SEQ ID NO:2), and/or SLT-2A (SEQ ID NO:3) wherein at least one amino acid is disrupted in the natively positioned epitope regions provided in the Examples (Tables 1, 2, 3, 4, and/or 5). Further embodiments are polypeptides comprising a de-immunized Shiga toxin effector region which is derived from amino acids 1 to 261 of SLT-1A (SEQ ID NO: l), StxA (SEQ ID NO: 2), and/or SLT-2A (SEQ ID NO:3) wherein at least one amino acid is disrupted in the natively positioned epitope regions provided in the Examples (Tables 1, 2, 3, 4, and/or 5).
[158] There are numerous, diverse, internal amino acid substitutions that can be used to create de-immunized Shiga toxin effector region polypeptides of the invention.
[159] Of the possible substitute amino acids to use within an epitope region, the following substitute amino acid residues are predicted to be the most likely to reduce the antigenicity and/or immunogenicity of an epitope— G, D, E, S, T, R, K, and H. Except for glycine, these residues all represent polar and/or charged residues.
[160] Of the possible amino acids to substitute with, the following amino acids A, G, V, L, I, P, C, M, F, S, D, N, Q, H, and K are predicted to be the most likely to reduce antigenicity and/or immunogenicity while retaining a significant Shiga toxin effector function depending on the amino acid substituted for. Generally, the substitution should change a polar and/or charged amino acid residue to a non-polar and uncharged residue. In addition, it may be beneficial to epitope disruption to reduce the overall amino acid residue's R-group functional side chain size and/or length. For example, alanine is generally an acceptable substitution for any amino acid residue, and, for glycine residues, alanine is the preferred choice. Serine is generally only an acceptable substitution for glutamate residues. Aspartate is generally only an acceptable substitution for glutamate residues. Lysine is generally only an acceptable substitution for arginine residues. Glutamine is generally only an acceptable substitution for glutamate, lysine, or arginine residues. Histidine is generally only an acceptable substitution for lysine and arginine residues. However despite these generalities of substitutions most likely to confer epitope disruption, because the aim is to preserve significant Shiga toxin effector function(s), the substitute amino acid might be more likely to preserve Shiga toxin effector function(s) if it resembles the amino acid substituted for, such as, e.g., a nonpolar and/or uncharged residue of similar size substituted for a polar and/or charged residue.
[161] Based on the empirical evidence in the Examples, certain amino acid positions in the A Subunits of Shiga toxins are predicted to tolerate epitope disruptions while still retaining significant Shiga toxin effector functions. For example, the following natively occurring positions tolerated amino acid substitutions, either alone or in combination, while retaining a Shiga toxin effector function(s) such as cytotoxicity— 1 of SEQ ID NO: l or SEQ ID NO:2; 4 of SEQ ID NO: 1, SEQ ID NO:2, or SEQ ID NO:3; 8 of SEQ ID NO: 1, SEQ ID NO:2, or SEQ ID NO:3; 9 of SEQ ID NO: 1, SEQ ID NO:2, or SEQ ID NO:3; 11 of SEQ ID NO: l, SEQ ID NO:2, or SEQ ID NO:3; 33 of SEQ ID NO: 1 or SEQ ID NO:2; 43 of SEQ ID NO: 1 or SEQ ID NO:2; 45 of SEQ ID NO: 1 or SEQ ID NO:2; 47 of SEQ ID NO: 1 or SEQ ID NO:2; 48 of SEQ ID NO: 1, SEQ ID NO:2, or SEQ ID NO:3; 49 of SEQ ID NO: 1 or SEQ ID NO:2; 53 of SEQ ID NO: 1 or SEQ ID NO:2; 55 of SEQ ID NO: 1 or SEQ ID NO:2; 58 of SEQ ID NO: 1, SEQ ID NO:2, or SEQ ID NO:3; 59 of SEQ ID NO: 1, SEQ ID NO:2, or SEQ ID NO:3; 60 of SEQ ID NO: l or SEQ ID NO:2; 61 of SEQ ID NO: l or SEQ ID NO:2; 62 of SEQ ID NO: 1 or SEQ ID NO:2; 94 of SEQ ID NO: 1, SEQ ID NO:2, or SEQ ID NO:3; 96 of SEQ ID NO: 1, SEQ ID NO:2, or SEQ ID NO : 3 ; 109 of SEQ ID NO : 1 , SEQ ID NO :2, or SEQ ID NO : 3 ; 110 of SEQ ID NO: l or SEQ ID NO:2; 112 of SEQ ID NO: l, SEQ ID NO:2, or SEQ ID NO:3; SE 147 of SEQ ID NO: l, SEQ ID NO:2, or SEQ ID NO:3; 179 of SEQ ID NO: l, SEQ ID NO:2, or SEQ ID NO:3; 180 of SEQ ID NO: l or SEQ ID NO:2; 181 of SEQ ID NO: 1 or SEQ ID NO:2; 183 of SEQ ID NO: 1, SEQ ID NO:2, or SEQ ID NO:3; 184 of SEQ ID NO: l, SEQ ID NO:2, or SEQ ID NO:3; 185 of SEQ ID NO: 1 or SEQ ID NO:2; 186 of SEQ ID NO: l, SEQ ID NO:2, or SEQ ID NO:3; 187 of SEQ ID NO: l or SEQ ID NO:2; 188 of SEQ ID NO: 1 or SEQ ID NO:2; 189 of SEQ ID NO: l or SEQ ID NO:2; 204 of SEQ ID NO:3; 205 of SEQ ID NO: 1 or SEQ ID NO:2; 247 of SEQ ID NO: 1 or SEQ ID NO:2; 247 of SEQ ID NO:3; 248 of SEQ ID NO: 1 or SEQ ID NO:2; 250 of SEQ ID NO:3; 251 of SEQ ID NO: 1 or SEQ ID NO:2; 264 of SEQ ID NO: 1, SEQ ID NO:2, or SEQ ID NO:3; 265 of SEQ ID NO: 1 or SEQ ID NO:2; and 286 of SEQ ID NO: 1 or SEQ ID NO:2.
[162] The empirical data in the Examples point towards other epitope disrupting substitutions and combinations of epitope disrupting substitutions that can reduce antigenicity and/or immunogenicity while retaining a significant Shiga toxin effector function such as, e.g., new combinations of the aforementioned truncations and positions tolerating substitutions as well as new substitutions at identical positions or conserved positions in related Shiga toxins.
[163] It is predictable that other amino acid substitutions to amino acid residues of a conservative functional group may reduce antigenicity and/or
immunogenicity while retaining a significant Shiga toxin effector function. For example, other substitutions known to the skilled worker to be similar to any of KIM, T4I, S8I, T8V, T9I, S9I, Kl 1A, Kl 1H, S33I, S45I, T45I, D47G, N48V, N48F, L49A, D53A, D53G, D53N, R55A, R55V, R55L, D58A, D58F, P59A, P59F, E60I, E60T, E60R, E61A, E61V, E61L, G62A, D94A, S96I, S109V, T109V, G110A, SI 12V, G147A, R179A, T180G, T181I, D183A, D183G, D184A, D184F, L185V, S186A, S186F, G187A, R188A, R188L, S189A, R204A, R205A, S247I, Y247A, R248A, R250A, R251A, D264A, G264A, T286A and/or T286I may disrupt an epitope while maintaining at least one Shiga toxin effector function. In particular, amino acid substitutions to conservative amino acid residues similar to KIM, T4I, S8I, T8V, T9I, S9I, Kl 1A, Kl 1H, S33I, S45I, T45I, D47G, N48V, N48F, L49A, D53A, D53G, D53N, R55A, R55V, R55L, D58A, D58F, Ρ59Α, P59F, E60I, E60T, E60R, E61A, E61V, E61L, G62A, D94A, S96I, S109V, T109V, G110A, SI 12V, G147A, R179A, T180G, T181I, D183A, D183G, D184A, D184F, L185V, S186A, S186F, G187A, R188A, R188L, S189A, R204A, R205A, S247I, Y247A, R248A,
R250A, R251A, D264A, G264A, T286A and/or T286I may have the same or similar effects. In certain embodiments, a Shiga toxin effector region polypeptide of the invention may comprise similar conservative amino acid substitutions such as, e.g., Kl to A, G, V, L, I, F, M and H; T4 to A, G, V, L, I, F, M, and S; S8 to A, G, V, I, L, F, and M; T9 to A, G, V, I, L, F, M, and S; S9 to A, G, V, L, I, F, and M; Kl 1 to A, G, V, L, I, F, M and H; S33 to A, G, V, L, I, F, and M; S45 to A, G, V, L, I, F, and M; T45 to A, G, V, L, I, F, and M; D47 to A, G, V, L, I, F, S, and Q; N48 to A, G, V, L, and M; L49 to A or G; D53 to A, G, V, L, I, F, S, and Q; R55 to A, G, V, L, I, F, M, Q, S, K, and H; D58 to A, G, V, L, I, F, S, and Q; Ρ59 to A, G, and F; E60 to A, G, V, L, I, F, S, Q, N, D, M, and R; E61 to A, G, V, L, I, F, S, Q, N, D, M, and R; G62 to A; D94 to A, G, V, L, I, F, S, and Q; S96 to A, G, V, I, L, F, and M; SI 09 to A, G, V, I, L, F, and M; T109 to A, G, V, I, L, F, M, and S; Gl 10 to A; SI 12 to A, G, V, L, I, F, and M; G147 to A; R179 to A, G, V, L, I, F, M, Q, S, K, and H; T180 to A, G, V, L, I, F, M, and S; T181 to A, G, V, L, I, F, M, and S; D183 to A, G, V, L, I, F, S, and Q; D184 to A, G, V, L, I, F, S, and Q; S186 to A, G, V, I, L, F, and M; G187 to A; R188 to A, G, V, L, I, F, M, Q, S, K, and H; SI 89 to A, G, V, I, L, F, and M; R204 to A, G, V, L, I, F, M, Q, S, K, and H; R205 to A, G, V, L, I, F, M, Q, S, K and H; S247 to A, G, V, I, L, F, and M; Y247 to A, G, V, L, I, F, and M; R248 to A, G, V, L, I, F, M, Q, S, K, and H; R250 to A, G, V, L, I, F, M, Q, S, K, and H; R251 to A, G, V, L, I, F, M, Q, S, K, and H; D264 to A, G, V, L, I, F, S, and Q; G264 to A; and T286 to A, G, V, L, I, F, M, and S.
[164] Similarly, amino acid substitutions which remove charge, polarity, and/or reduce side chain length can disrupt an epitope while maintaining at least one Shiga toxin effector function. In certain embodiments, a Shiga toxin effector region polypeptide of the invention may comprise one or more epitopes disrupted by substitutions such that side chain charge is removed, polarity is removed, and/or side chain length is reduced such as, e.g., substituting the appropriate amino acid selected from the following group A, G, V, L, I, P, C, M, F, S, D, N, Q, H, or K for the amino acid residue at position 1 of SEQ ID NO: 1 or SEQ ID NO:2; 4 of SEQ ID NO: l, SEQ ID NO:2, or SEQ ID NO:3; 8 of SEQ ID NO: 1, SEQ ID NO:2, or SEQ ID NO:3; 9 of SEQ ID NO: 1, SEQ ID NO:2, or SEQ ID NO:3; 11 of SEQ ID NO:l, SEQ ID NO:2, or SEQ ID NO:3; 33 of SEQ ID NO: 1 or SEQ ID NO:2; 43 of SEQ ID NO: 1 or SEQ ID NO:2; 45 of SEQ ID NO: 1 or SEQ ID NO:2; 47 of SEQ ID NO: 1 or SEQ ID NO:2; 48 of SEQ ID NO: 1, SEQ ID NO: 2, or SEQ ID NO:3; 49 of SEQ ID NO:l or SEQ ID NO:2; 53 of SEQ ID NO: 1 or SEQ ID NO:2; 55 of SEQ ID NO: 1 or SEQ ID NO:2; 58 of SEQ ID NO:l, SEQ ID NO:2, or SEQ ID NO:3; 59 of SEQ ID NO: 1, SEQ ID NO:2, or SEQ ID NO:3; 60 of SEQ ID NO: 1 or SEQ ID NO:2; 61 of SEQ ID NO: 1 or SEQ ID NO:2; 62 of SEQ ID NO: 1 or SEQ ID NO:2; 94 of SEQ ID NO: l, SEQ ID NO:2, or SEQ ID NO:3; 96 of SEQ ID NO: l, SEQ ID NO:2, or SEQ ID NO:3; 109 of SEQ ID NO: 1, SEQ ID NO:2, or SEQ ID NO:3; 110 of SEQ ID NO: 1 or SEQ ID NO:2; 112 of SEQ ID NO: 1, SEQ ID NO:2, or SEQ ID NO:3; SE 147 of SEQ ID NO: 1, SEQ ID NO:2, or SEQ ID NO:3; 179 of SEQ ID NO : 1 , SEQ ID NO :2, or SEQ ID NO : 3 ; 180 of SEQ ID NO : 1 or SEQ ID NO:2; 181 of SEQ ID NO: l or SEQ ID NO:2; 183 of SEQ ID NO: l, SEQ ID NO:2, or SEQ ID NO:3; 184 of SEQ ID NO: l, SEQ ID NO:2, or SEQ ID NO:3; 185 of SEQ ID NO: 1 or SEQ ID NO:2; 186 of SEQ ID NO: l, SEQ ID NO:2, or SEQ ID O:3; 187 of SEQ ID NO: 1 or SEQ ID O:2; 188 of SEQ ID O: l or SEQ ID NO:2; 189 of SEQ ID NO: l or SEQ ID NO:2; 204 of SEQ ID NO:3; 205 of SEQ ID NO: 1 or SEQ ID NO:2; 247 of SEQ ID NO: 1 or SEQ ID NO:2; 247 of SEQ ID NO:3; 248 of SEQ ID NO: 1 or SEQ ID NO:2; 250 of SEQ ID NO:3; 251 of SEQ ID NO: 1 or SEQ ID NO :2; 264 of SEQ ID NO: 1, SEQ ID NO:2, or SEQ ID NO:3; 265 of SEQ ID NO: l or SEQ ID NO:2; and 286 of SEQ ID NO: 1 or SEQ ID NO:2. In certain embodiments, a Shiga toxin effector region polypeptide of the invention may comprise one or more of the following amino acid substitutions: Kl to A, G, V, L, I, F, M and H; T4 to A, G, V, L, I, F, M, and S; S8 to A, G, V, I, L, F, and M; T9 to A, G, V, I, L, F, M, and S; S9 to A, G, V, L, I, F, and M; Kl 1 to A, G, V, L, I, F, M and H; S33 to A, G, V, L, I, F, and M; S45 to A, G, V, L, I, F, and M; T45 to A, G, V, L, I, F, and M; D47 to A, G, V, L, I, F, S, and Q; N48 to A, G, V, L, and M; L49 to A or G; D53 to A, G, V, L, I, F, S, and Q; R55 to A, G, V, L, I, F, M, Q, S, K, and H; D58 to A, G, V, L, I, F, S, and Q; P59 to A, G, and F; E60 to A, G, V, L, I, F, S, Q, N, D, M, and R; E61 to A, G, V, L, I, F, S, Q, N, D, M, and R; G62 to A; D94 to A, G, V, L, I, F, S, and Q; S96 to A, G, V, I, L, F, and M; S109 to A, G, V, I, L, F, and M; T109 to A, G, V, I, L, F, M, and S; Gl 10 to A; SI 12 to A, G, V, L, I, F, and M; G147 to A; R179 to A, G, V, L, I, F, M, Q, S, K, and H; T180 to A, G, V, L, I, F, M, and S; T181 to A, G, V, L, I, F, M, and S; D183 to A, G, V, L, I, F, S, and Q; D184 to A, G, V, L, I, F, S, and Q; S186 to A, G, V, I, L, F, and M; G187 to A; R188 to A, G, V, L, I, F, M, Q, S, K, and H; SI 89 to A, G, V, I, L, F, and M; R204 to A, G, V, L, I, F, M, Q, S, K, and H; R205 to A, G, V, L, I, F, M, Q, S, K and H; S247 to A, G, V, I, L, F, and M; Y247 to A, G, V, L, I, F, and M; R248 to A, G, V, L, I, F, M, Q, S, K, and H; R250 to A, G, V, L, I, F, M, Q, S, K, and H; R251 to A, G, V, L, I, F, M, Q, S, K, and H; D264 to A, G, V, L, I, F, S, and Q; G264 to A; and T286 to A, G, V, L, I, F, M, and S.
[165] In addition, any amino acid substitution in one epitope region of a Shiga toxin effector polypeptide which disrupts an epitope while retaining significant Shiga toxin effector function is combinable with any other amino acid substitution in the same or a different epitope region which disrupts an epitope while retaining significant Shiga toxin effector function to form a de-immunized Shiga toxin effector polypeptide with multiple epitope regions disrupted while still retaining a significant level of Shiga toxin effector function. In certain embodiments, a Shiga toxin effector region polypeptide of the invention may comprise one or more of the following combinations: KIM may be combined with S8I, T9I, Kl 1A, S33I, S45I, T45I, D53A, R55A, D58A, D58F, P59A, E60I, E60R, E61A, G62A, D94A, S96I, G110A, G147A, T180G, T181I, D183A, D184A, D184F, S186A, G187A, R188A, S189A, R204A, R205A,
S247I, D264A, G264A, G265A, and/or T286I; S8I may be combined with KIM, T9I, Kl lA, S45I, T45I, D53A, R55A, D58A, D58F, P59A, E60I, E60R, E61A, G62A, D94A, S96I, G110A, G147A, T180G, T181I, D183A, D184A, D184F, S186A, G187A, R188A, S189A, R204A, R205A, S247I, D264A, G264A, G265A, and/or T286I; T9I may be combined with KIM, S8I, Kl 1A, S45I, T45I, D53A, R55A, D58A, D58F, P59A, E60I, E60R, E61A, G62A, D94A, S96I, G110A, G147A, T180G, T181I, D183A, D184A, D184F, S186A, G187A, R188A, S189A, R204A, R205A, S247I, D264A, G264A, G265A, and/or T286I; S9I may be combined with KIM, S8I, T9I, Kl 1A, S33I, S45I, T45I, D53A, R55A, D58A, D58F, P59A, E60I, E60R, E61A, G62A, D94A, S96I, Gl 10A, G147A, T180G, T181I, D183A, D184A, D184F, S186A, G187A, R188A, S189A, R204A, R205A, S247I, D264A, G264A, G265A, and/or T286I; Kl lA may be combined with KIM, S8I, T9I, Kl 1A, S45I, T45I, D53A, R55A, D58A, D58F, P59A, E60I, E60R, E61A, G62A, D94A, S96I, G110A, G147A, T180G, T181I, D183A, D184A, D184F, S186A, G187A, R188A, S189A, R204A,
R205A, S247I, D264A, G264A, G265A, and/or T286I; S33I may be combined with KIM, S8I, T9I, Kl lA, S45I, T45I, D53A, R55A, D58A, D58F, P59A, E60I, E60R, E61A, G62A, D94A, S96I, G110A, G147A, T180G, T181I, D183A, D184A, D184F, S186A, G187A, R188A, S189A, R204A, R205A, S247I, D264A, G264A, G265A, and/or T286I; S45V or S45I may be combined with KIM, S8I, T9I, Kl lA, S33I, D53A, R55A, D58A, D58F, P59A, E60I, E60R, E61A, G62A, D94A, S96I, G110A, G147A, T180G, T181I, D183A, D184A, D184F, S186A, G187A, R188A, S189A, R204A, R205A, S247I, D264A, G264A, G265A, and/or T286I; T45I may be combined with KIM, S8I, T9I, Kl 1A, S33I, D53A, R55A, D58A, D58F, P59A, E60I, E60R, E61A, G62A, D94A, S96I, G110A, G147A, T180G, T181I, D183A, D184A, D184F, S186A, G187A, R188A, S189A, R204A, R205A, S247I, D264A, G264A, G265A, and/or T286I; D53A may be combined with KIM, S8I, T9I, Kl 1A, S33I, S45I, T45I, R55A, D58A, D58F, P59A, E60I, E60R, E61A, G62A, D94A, S96I, Gl lOA, G147A, T180G, T181I, D183A, D184A, D184F, S186A, G187A, R188A, S189A, R204A, R205A, S247I, D264A, G264A, G265A, and/or T286I; R55A KIM, S8I, T9I, Kl 1A, S33I, S45I, T45I, D53A, R55A, D58A, D58F, P59A, E60I, E60R, E61A, G62A, D94A, S96I, Gl lOA, G147A, T180G, T181I, D183A, D184A, D184F, S186A, G187A, R188A, S189A, R204A, R205A,
S247I, D264A, G264A, G265A, and/or T286I; D58A or D58F may be combined with KIM, S8I, T9I, K11A, S33I, S45I, T45I, D53A, R55A, P59A, E60I, E60R, E61A, G62A, Gl lOA, D94A, S96I, G147A, T180G, T181I, D183A, D184A, D184F, S186A, G187A, R188A, S189A, R204A, R205A, S247I, D264A, G264A, G265A, and/or T286I; R55A may be combined with KIM, S8I, T9I,
Kl 1A, S33I, S45I, T45I, D53A, D58A, D58F, P59A, E60I, E60R, E61A, G62A, D94A, S96I, Gl lOA, G147A, T180G, T181I, D183A, D184A, D184F, S186A, G187A, R188A, S189A, R204A, R205A, S247I, D264A, G264A, G265A, and/or T286I; P59A may be combined with KIM, S8I, T9I, Kl 1A, S33I, S45I, T45I, D53A, R55A, D58A, D58F, E60I, E60R, E61A, G62A, D94A, S96I, Gl lOA, G147A, T180G, T181I, D183A, D184A, D184F, S186A, G187A, R188A, S189A, R204A, R205A, S247I, D264A, G264A, G265A, and/or T286I; E60R may be combined with KIM, S8I, T9I, Kl 1A, S33I, S45I, T45I, D53A, R55A, D58A, D58F, P59A, E61A, G62A, D94A, S96I, Gl lOA, G147A, T180G, T181I, D183A, D184A, D184F, S186A, G187A, R188A, S189A, R204A,
R205A, S247I, D264A, G264A, G265A, and/or T286I; E60I or E60A may be combined with KIM, S8I, T9I, Kl 1A, S45I, T45I, D53A, R55A, D58A, D58F, P59A, E61A, G62A, D94A, S96I, Gl lOA, G147A, T180G, T181I, D183A, D184A, D184F, S186A, G187A, R188A, S189A, R204A, R205A, S247I, D264A, G264A, G265A, and/or T286I; E61A may be combined with KIM, S8I, T9I, K11A, S45I, T45I, D53A, R55A, D58A, D58F, P59A, E60I, E60R, G62A, D94A, S96I, Gl lOA, G147A, T180G, T181I, D183A, D184A, D184F, S186A, G187A, R188A, S189A, R204A, R205A, S247I, D264A, G264A, G265A, and/or T286I; G62A may be combined with KIM, S8I, T9I, Kl 1A, S45I, T45I, D53A, R55A, D58A, D58F, P59A, E60I, E60R, E61A, D94A, S96I, Gl 10A, G147A, T180G, T181I, D183A, D184A, D184F, S186A, G187A, R188A, S189A, R204A, R205A, S247I, D264A, G264A, G265A, and/or T286I; D94A may be combined with KIM, T9I, Kl 1A, S33I, S45I, T45I, D53A, R55A, D58A, D58F, P59A, E60I, E60R, E61A, G62A, D94A, S96I, Gl lOA, G147A, T180G, T181I, D183A, D184A, D184F, S186A, G187A, R188A, S189A, R204A, R205A, S247I, D264A, G264A, G265A, and/or T286I; S96I may be combined with KIM, T9I, Kl 1A, S33I, S45I, T45I, D53A, R55A, D58A, D58F, P59A, E60I, E60R, E61A, G62A, D94A, S96I, G110A, G147A, T180G, T181I, D183A, D184A, D184F, S186A, G187A, R188A, S189A, R204A, R205A, S247I, D264A, G264A, G265A, and/or T286I; Gl 10A may be combined with KIM, T9I, K11A, S33I, S45I, T45I, D53A, R55A, D58A, D58F, P59A, E60I, E60R, E61A, G62A, D94A, S96I, G147A, T180G, T181I, D183A, D184A, D184F, S186A, G187A, R188A, S189A, R204A, R205A, S247I, D264A, G264A, G265A, and/or T286I; G147A may be combined with KIM, T9I, Kl 1A, S33I, S45I, T45I, D53A, R55A, D58A, D58F, P59A, E60I, E60R, E61A, G62A, D94A, S96I, G110A, T180G, T181I, D183A, D184A, D184F, S186A, G187A, R188A, S189A, R204A, R205A, S247I, D264A, G264A, G265A, and/or T286I; T180G may be combined with KIM, S8I, T9I, Kl 1A, S33I, S45I, T45I, D53A, R55A, D58A, D58F, P59A, E60I, E60R, E61A, G62A, D94A, S96I, Gl 10A, G147A, T181I, D183A, D184A, D184F, S186A, G187A, R188A, S189A, R204A, R205A, S247I, D264A, G264A, G265A, and/or T286I; Tl 8 II may be combined with KIM, S8I, T9I, Kl 1A, S45I, T45I, D53A, R55A, D58A, D58F, P59A, E60I, E60R, E61A, G62A, D94A, S96I, Gl 10A, G147A, T180G, D183A, D184A, D184F, S186A, G187A, R188A, S189A, R204A, R205A,
S247I, D264A, G264A, G265A, and/or T286I; D183A may be combined with KIM, S8I, T9I, K11A, S33I, S45I, T45I, D53A, R55A, D58A, D58F, P59A, E60I, E60R, E61A, G62A, D94A, S96I, G110A, G147A, T180G, T181I, D184A, D184F, S186A, G187A, R188A, S189A, R204A, R205A, S247I, D264A, G264A, G265A, and/or T286I; D184A or D184F may be combined with KIM, S8I, T9I, K11A, S33I, S45I, T45I, D53A, R55A, D58A, D58F, P59A, E60I, E60R, E61A, G62A, D94A, S96I, G110A, G147A, T180G, T181I, D183A, S186A, G187A, R188A, S189A, R204A, R205A, S247I, D264A, G264A, G265A, and/or T286I; R204A may be combined with KIM, S8I, T9I, Kl 1A, S33I, S45I, T45I, D53A, R55A, D58A, D58F, P59A, E60I, E60R, E61A, G62A, D94A, S96I, G110A, G147A, T180G, T181I, D183A, D184A, D184F, S186A, G187A, R188A, S189A, R205A, S247I, D264A, G264A, G265A, and/or T286I; R205A may be combined with KIM, S8I, T9I, Kl 1A, S33I, S45I, T45I, D53A, R55A, D58A, D58F, P59A, E60I, E60R, E61A, G62A, D94A, S96I, G110A, G147A, T180G, T181I, D183A, D184A, D184F, S186A, G187A, R188A, S189A, R204A, S247I, D264A, G264A, G265A, and/or T286I; S247I may be combined with KIM, S8I, T9I, Kl 1A, S45I, T45I, D53A, R55A, D58A, D58F, P59A, E60I, E60R, E61A, G62A, D94A, S96I, G110A, G147A, T180G, T181I, D183A, D184A, D184F, S186A, G187A, R188A, S189A, R204A,
R205A, D264A, G264A, G265A, and/or T286I; D264A may be combined with KIM, S8I, T9I, K11A, S45I, T45I, D53A, R55A, D58A, D58F, P59A, E60I, E60R, E61A, G62A, D94A, S96I, G110A, G147A, T180G, T181I, D183A, D184A, D184F, S186A, G187A, R188A, S189A, R204A, R205A, S247I, G264A, G265A, and/or T286I; G264A may be combined with KIM, S8I, T9I, Kl 1A, S45I, T45I, D53A, R55A, D58A, D58F, P59A, E60I, E60R, E61A, G62A, D94A, S96I, G110A, G147A, T180G, T181I, D183A, D184A, D184F, S186A, G187A, R188A, S189A, R204A, R205A, S247I, D264A, G265A, and/or T286I; G265A may be combined with KIM, S8I, T9I, Kl 1A, S45I, T45I, D53A, R55A, D58A, D58F, P59A, E60I, E60R, E61A, G62A, D94A, S96I, Gl 10A, G147A, T180G, T181I, D183A, D184A, D184F, S186A, G187A, R188A, S189A, R204A, R205A, S247I, D264A, G264A, and/or T286I; and/or T286I may be combined with KIM, S8I, T9I, Kl 1A, S45I, T45I, D53A, R55A, D58A, D58F, P59A, E60I, E60R, E61A, G62A, D94A, S96I, G110A, G147A, T180G, T181I, D183A, D184A, D184F, S186A, G187A, R188A, S189A, R204A, R205A, S247I, D264A, G264A, and/or G265A.
[166] Based on the empirical evidence in the Examples, certain amino acid regions in the A Subunits of Shiga toxins are predicted to tolerate epitope disruptions while still retaining significant Shiga toxin effector functions. For example, the epitope regions natively positioned at 1-15, 53-66, 55-66, 94-115 and 180-190 tolerated multiple amino acid substitution combinations simultaneously without losing Shiga toxin enzymatic activity and often without losing cytotoxicity (see Examples).
[167] The linking of cell targeting binding regions with de-immunized Shiga toxin effector region polypeptides enables the engineering of cell-type specific targeting of the potent Shiga toxin cytotoxicity with fewer potential adverse effects resulting from antigenicity and/or immunogenicity when administered to a mammal, e.g., a human subject. Proteins of the invention comprise de- immunized Shiga toxin effector regions derived from the A Subunits of members of the Shiga toxin family linked to binding regions which can bind specifically to at least one extracellular target biomolecule in physical association with a cell, such as a target biomolecule expressed on the surface of a cell. This general structure is modular in that any number of diverse cell-targeting binding regions may be linked to the de-immunized Shiga toxin effector region polypeptides of the invention.
[168] Among certain embodiments of the present invention, the proteins comprise a binding region derived from an immunoglobulin-type polypeptide selected for specific and high-affinity binding to a surface antigen on the cell surface of a cancer cell, where the antigen is restricted in expression to cancer cells (see Glokler J et al, Molecules 15: 2478-90 (2010); Liu Y et al, Lab Chip 9: 1033-6 (2009). In accordance with other embodiments, the binding region is selected for specific and high-affinity binding to a surface antigen on the cell surface of a cancer cell, where the antigen is over-expressed or preferentially expressed by cancer cells as compared to non-cancer cells. Some representative target biomolecules include, but are not limited to, the following enumerated targets associated with cancers and/or specific immune cell types.
[169] Many immunoglobulin-type binding regions that recognize epitopes associated with cancer cells exist in the prior art, such as binding regions that target annexin Al, B3 melanoma antigen, B4 melanoma antigen, CD2, CD3,
CD4, CD20 (B-lymphocyte antigen protein CD20), CD22, CD25 (interleukin-2 receptor IL2R), CD30 (TNFRSF8), CD38 (cyclic ADP ribose hydrolase), CD40, CD44 (hyaluronan receptor), ITGAV (CD51), CD66, CD71 (transferrin receptor), CD73, CD74 (HLA-DR antigens-associated invariant chain), CD79, CD98, endoglin (END, CD 105), CD 106 (VCAM-1), chemokine receptor type 4 (CDCR-4, fusin, CD 184), CD200, insulin-like growth factor 1 receptor
(CD221), mucin 1 (MUC1, CD227), basal cell adhesion molecule (B-CAM, CD239), CD248 (endosialin, TEM1), tumor necrosis factor receptor 10b (TNFRSF10B, CD262), tumor necrosis factor receptor 13B (TNFRSF 13B, TACI, CD276), vascular endothelial growth factor receptor 2 (KDR, CD309), epithelial cell adhesion molecule (EpCAM, CD326), human epidermal growth factor receptor 2 (HER2, Neu, ErbB2, CD340), cancer antigen 15-3 (CA15-3), cancer antigen 19-9 (CA 19-9), cancer antigen 125 (CA125, MUC16), CA242, carcinoembryonic antigen-related cell adhesion molecules (e.g. CEACAM3 (CD66d) and CEACAM5), carcinoembryonic antigen protein (CEA), chondroitin sulfate proteoglycan 4 (CSP4, MCSP, NG2), CTLA4, DLL4, epidermal growth factor receptor (EGFR, ErbBl), folate receptor (FOLR), G-28, ganglioside GD2, ganglioside GD3, HLA-DrlO, HLA-DRB, human epidermal growth factor receptor 1 (HER1), Ephrin type-B receptor 2 (EphB2), epithelial cell adhesion molecule (EpCAM), fibroblast activation protein (FAP/seprase), insulin-like growth factor 1 receptor (IGF1R), interleukin 2 receptor (IL-2R), interleukin 6 receptor (IL-6R), integrins alpha-V beta-3 (ανβ3), integrins alpha-V beta-5 (ανβ5), integrins alpha-5 beta-1 (ουβι), L6, MPG, melanoma-associated antigen 1 protein (MAGE-1), melanoma-associated antigen 3 (MAGE-3), mesothelin (MSLN), MPG, MS4A, p21, p97, polio virus receptor-like 4
(PVRL4), protease-activated-receptors (such as PARI), prostate-specific membrane antigen protein (PSMA), trophoblast glycoprotein (TPGB), and tumor-associated calcium signal transducers (TACSTDs) (see e.g. Lui B et al., Cancer Res 64: 704-10 (2004); Novellino L et al, Cancer Immunol Immunother 54: 187-207 (2005); Bagley R et al, Int JOncol 34: 619-27 (2009); Gerber H et al, mAbs 1: 247-53 (2009); Beck A et al, Nat Rev Immunol 10: 345-52 (2010); Andersen J et al, J Biol Chem 287: 22927-37 (2012); Nolan-Stevaux O et al, PLoS One 7: e50920 (2012); Rust S et al., Mol Cancer 12: 11 (2013)). This list of target biomolecules is intended to be non-limiting. It will be appreciated by the skilled worker that any desired target biomolecule associated with a cancer cell or other desired cell type may be used to design or select a binding region to be coupled with the Shiga toxin effector region to produce a protein of the invention.
[ 170] Examples of other target biomolecules which are strongly associated with cancer cells and immunoglobulin-type binding regions known to bind them include BAGE proteins (B melanoma antigens), basal cell adhesion molecules (BCAMs or Lutheran blood group glycoproteins), bladder tumor antigen (BTA), cancer-testis antigen NY-ESO-1, cancer-testis antigen LAGE proteins, CD 19 (B- lymphocyte antigen protein CD 19), CD21 (complement receptor-2 or complement 3d receptor), CD26 (dipeptidyl peptidase-4, DPP4, or adenosine deaminase complexing protein 2), CD33 (sialic acid-binding immunoglobulin- type lectin-3), CD52 (CAMPATH-1 antigen), CD56, CS1 (SLAM family number 7 or SLAMF7), cell surface A33 antigen protein (gpA33), Epstein-Barr Virus antigen proteins, GAGE/PAGE proteins (melanoma associated cancer/testis antigens), hepatocyte growth factor receptor (HGFR or c-Met), MAGE proteins, melanoma antigen recognized by T-cells 1 protein (MART- 1/MelanA, MARTI), mucins, Preferentially Expressed Antigen of Melanoma (PRAME) proteins, prostate specific antigen protein (PSA), prostate stem cell antigen protein (PSCA), Receptor for Advanced Glycation Endroducts (RAGE), tumor-associated glycoprotein 72 (TAG-72), vascular endothelial growth factor receptors (VEGFRs), and Wilms' tumor antigen.
[171] Examples of other target biomolecules which are strongly associated with cancer cells are carbonic anhydrase IX (CA9/CAIX), Claudin proteins (CLDN3, CLDN4), ephrin type-A receptor 3 (EphA3), folate binding proteins (FBP), ganglioside GM2, insulin-like growth factor receptors, integrins (such as CDl la- c), receptor activator of nuclear factor kappa B (RANK), receptor tyrosine- protein kinase erB-3, tumor necrosis factor receptor 10A (TRAIL-R1/DR4), tumor necrosis factor receptor 10B (TRAIL-R2), Tenascin C, and CD64 (FcyRI) (see Hough C et al, Cancer Res 60: 6281-7 (2000); Thepen T et al, Nat Biotechnol 18: 48-51 (2000); Pastan I et al, Nat Rev Cancer 6: 559-65 (2006); Pastan, Annu Rev Med 58: 221-37 (2007); Fitzgerald D et al, Cancer Res 71 : 6300-9 (2011); Scott A et al, Cancer Immun 12: 14-22 (2012)). This list of target biomolecules is intended to be non-limiting.
[172] In addition, there are numerous other examples of contemplated, target biomolecules such as ADAM metalloproteinases (e.g. ADAM-9, ADAM- 10, ADAM- 12, ADAM- 15, ADAM- 17), ADP-ribosyltransferases (ART1, ART4), antigen F4/80, bone marrow stroma antigens (BST1, BST2), break point cluster region-c-abl oncogene (BCR-ABL) proteins, C3aR (complement component 3a receptors), CD7, CD 13, CD 14, CD 15 (Lewis X or stage-specific embryonic antigen 1), CD23 (FC epsilon RII), CD49d, CD53, CD54 (intercellular adhesion molecule 1), CD63 (tetraspanin), CD69, CD80, CD86, CD88 (complement component 5a receptor 1), CDl 15 (colony stimulating factor 1 receptor), CD123 (interleukin-3 receptor), CD 129 (interleukin 9 receptor), CD 183 (chemokine receptor CXCR3), CD191 (CCR1), CD193 (CCR3), CD195 (chemokine receptor CCR5), CD203c, CD225 (interferon-induced transmembrane protein 1), CD244 (Natural Killer Cell Receptor 2B4), CD282 (toll-like receptor 2), CD284 (Toll-like receptor 4), CD294 (GPR44), CD305 (leukocyte-associated immunoglobulin-like receptor 1), ephrin type-A receptor 2 (EphA2), FceRIa, galectin-9, alpha- fetoprotein antigen 17-A1 protein, human aspartyl
(asparaginyl) beta-hydroxylase (HAAH), immunoglobulin-like transcript ILT-3, lysophosphatidlglycerol acyltransferase 1 (LPGAT1/IAA0205), lysosome- associated membrane proteins (LAMPs, such as CD 107), melanocyte protein PMEL (gplOO), myeloid-related protein- 14 (mrp-14), receptor tyrosine-protein kinase erbB-3, SART proteins, scavenger receptors (such as CD64 and CD68), Siglecs (sialic acid-binding immunoglobulin-type lectins), syndecans (such as SDC1 or CD138), tyrosinase, tyrosinease-related protein 1 (TRP-1), tyrosinease- related protein 2 (TRP-2), tyrosinase associated antigen (TAA), APO-3, BCMA, CD2, CD3, CD4, CD8, CD18, CD27, CD28, CD29, CD41, CD49, CD90, CD95 (Fas), CD103, CD104, CD134 (OX40), CD137 (4-1BB), CD152 (CTLA-4), chemokine receptors, complement proteins, cytokine receptors,
histocompatibility proteins, ICOS, interferon-alpha, interferon-beta, c-myc, osteoprotegerin, PD-1, RANK, TACI, TNF receptor superfamily member (TNF- Rl, TNFR-2), Apo2/TRAIL-Rl, TRAIL-R2, TRAIL-R3, and TRAIL-R4 (see Scott A et al, Cancer Immunity 12: 14 (2012); Cheever M et al, Clin Cancer Res 15: 5323-37 (2009)), for target biomolecules and note the target molecules described therein are non-limiting examples). It will be appreciated by the skilled worker that any desired target biomolecule may be used to design or select a binding region to be coupled with a de-immunized Shiga toxin effector region to produce a protein of the invention.
[173] In certain embodiments, the binding region comprises or consists essentially of an immunoglobulin-type polypeptide selected for specific and high-affinity binding to the cellular surface of a cell type of the immune system. For example, immunoglobulin-type binding domains are known that bind to CD1, CD2, CD3, CD4, CD5, CD6, CD7, CD8, CD9, CD10, CD11, CD12, CD13, CD14, CD15, CD16, CD17, CD18, CD19, CD20, CD21, CD22, CD23, CD24, CD25, CD26, CD27, CD28, CD29, CD30, CD31, CD33, CD34, CD35, CD36, CD37, CD38, CD40, CD41, CD56, CD61, CD62, CD66, CD95, CD117, CD 123, CD235, CD 146, CD326, interleukin-2 receptor (IL-2R), receptor activator of nuclear factor kappa B (RANKL), SLAM-associated protein (SAP), and TNFSF18 (tumor necrosis factor ligand 18 or GITRL). [174] For certain embodiments, the de-immunized cytotoxic protein comprises or consists essentially of amino acids of SEQ ID NO:53, SEQ ID NO:54, SEQ ID NO:55, or SEQ ID NO:56. These de-immunized CD20-binding cytotoxic protein embodiments may be used to treat and/or diagnosis bone cancer, leukemia, lymphoma, melanoma, myeloma, amyloidosis, ankylosing spondylitis, asthma, Crohn's disease, diabetes, graft rejection, graft-versus-host disease, Hashimoto's thyroiditis, hemolytic uremic syndrome, HIV-related diseases, lupus erythematosus, multiple sclerosis, polyarteritis, psoriasis, psoriatic arthritis, rheumatoid arthritis, scleroderma, septic shock, Sjorgren's syndrome, ulcerative colitis, and/or vasculitis.
[175] For certain embodiments, the de-immunized cytotoxic protein comprises or consists essentially of amino acids of SEQ ID NO:57, SEQ ID NO:58, or SEQ ID NO:59. These de-immunized HER-2-binding cytotoxic protein embodiments may be used to treat and/or diagnosis of breast cancer, cervical cancer, head- neck cancer (e.g. oropharynx), gastrointestinal cancer (e.g. esophageal and colorectal), kidney-urinary tract cancer (e.g. bladder), lung/pleura cancer, and ovarian cancer.
[176] In certain embodiments, the binding region comprises or consists essentially of a ligand selected for targeting an extracellular receptor. Some representative ligands include, but are not limited to, the following bone morphogenetic proteins and activin membrane-bound inhibitor BAMBI (also known as TGFBR), CD137L (also known as 4- IBB), decoy receptor 3 DcR3 (also known as TR6 and TNFRSF6B), and the tumor necrosis factor TWEAK (also known as TNFSF12 and AP03L). For more non-limiting exemplary ligands, see Table 12 in the Examples.
[177] De-immunized Shiga toxin effector regions which become non-toxic after epitope disruption, e.g. Shiga toxin effector regions comprising R179A, may still be useful for delivering exogenous materials into cells. De-immunized Shiga toxin effector regions which retain only a significant level of the Shiga toxin function of catalytic activity are still useful as enzymatically active, de- immunized components of molecules.
[178] It is within the scope of the invention to use fragments, variants, and/or derivatives of the polypeptides and proteins of the invention which contain a functional extracellular target biomolecule binding site, and even more preferably capable of binding the target biomolecule with high affinity (e.g. as shown by KD). For example, any binding region comprising a polypeptide that binds to a target biomolecule, preferably expressed on a cell surface, with a dissociation constant of 10"5 to 10"12 moles per liter, preferably less than 200 nM, may be substituted for use in making molecules of the invention (e.g. de- immunized Shiga toxin effector polypeptides and cytotoxic proteins) and methods of the invention.
IV. General Functions of the De-Immunized Shiga Toxin Effector Region Polypeptides and Proteins
[179] The polypeptides and proteins of the invention have improved usefulness for administration to mammalian species as either a therapeutic and/or diagnostic agent because of the reduced likelihood of producing undesired immune responses in mammals. Importantly, in polypeptides of the invention, the desired biological functions of the original Shiga toxin effector regions were preserved after the B-cell epitope(s) was disrupted. In addition, B-cell epitopes often coincide or overlap with epitopes of mature CD4+ T-cells, thus the disruption of a B-cell epitope often simultaneously disrupts a CD4+ T-cell epitope.
[180] The various de-immunized Shiga toxin effector polypeptides of the invention might differ in their antigenicity profiles when administered to various mammals, but are expected to have reduced antigenicity and/or immunogenicity. It is not necessary to completely eliminate all immunogenicity from a Shiga toxin derived polypeptide in order to improve its use in medical applications involving administration to a mammal (see Nagata, Adv Drug Deliv Rev 61 : 977- 85 (2009)). The modification of only a few dominant amino acids in a therapeutic protein can greatly reduce its antigenicity and/or immunogenicity without perturbing the protein's overall stability, structure, and function.
However, Shiga toxin effector polypeptide regions with disruptions in more immunogenic B-cell epitopes are expected to be more advantageous for administration to mammals when it is desirable to avoid unwanted B-cell and/or CD4+ T-cell immune responses.
[181] The present invention provides various de-immunized Shiga toxin effector polypeptides which may be used as components of various compositions of matter, such as cell-targeted cytotoxic proteins and diagnostic compositions. In particular, the de-immunized Shiga toxin effector polypeptides have uses as components of various protein therapeutics, such as, e.g. immunotoxins and ligand-toxin fusions, for the targeted killing of specific cell types for the treatment of a variety of diseases, including cancers, immune disorders, and microbial infections.
[182] The present invention also provides various cytotoxic proteins comprising de-immunized Shiga toxin effector regions functionally associated with binding regions to effectuate cell targeting such that the cytotoxic proteins selectively kill, inhibit the growth of, deliver exogenous material to and/or detect specific cell types. The binding regions of the proteins of the invention are capable of binding specifically to at least one extracellular target biomolecule in physical association with a cell, such as a target biomolecule expressed on the surface of a cell. The linking of cell targeting binding regions with de- immunized Shiga toxin effector region polypeptides enables the engineering of cell-type specific targeting of the potent Shiga toxin cytotoxicity and/or cytostasis.
[183] In certain embodiments, the proteins of the invention are capable of binding extracellular target biomolecules associated with the cell surface of particular cell types and entering those cells. Once internalized within a targeted cell type, certain embodiments of the proteins of the invention are capable of routing an enzymatically active, cytotoxic, Shiga toxin effector polypeptide fragment into the cytosol of the target cell. Once in the cytosol of a targeted cell type, certain embodiments of the cytotoxic proteins of the invention are capable of enzymatically inactivating ribosomes and eventually killing the cell.
Alternatively, nontoxic variants of the proteins of the invention may be used to deliver additional exogenous materials into target cells, such as peptides, polypeptides, proteins, polynucleotides, and detection promoting agents. This system is modular, in that any number of diverse binding regions can be used to target this potent cytotoxicity to various, diverse cell types.
A. Cell Kill via Targeted Shiga Toxin Cytotoxicity
[ 184] Because members of the Shiga toxin family are adapted to killing eukaryotic cells, cytotoxic proteins designed using de-immunized Shiga toxin effector regions can show potent cell-kill activity. The A Subunits of members of the Shiga toxin family comprise enzymatic domains capable of killing a eukaryotic cell once in the cell's cytosol. The disruption of B-cell epitopes did not significantly alter the cytotoxic mechanism of certain Shiga toxin effector regions of the invention. Thus, the de-immunized cytotoxic proteins of the invention maintain potent cytotoxicity while reducing the likelihood of certain immune responses when administered to a mammal.
[185] In certain embodiments of the de-immunized cytotoxic proteins of the invention, upon contacting a cell physically coupled with an extracellular target biomolecule of the binding region of a cytotoxic protein of the invention (target+ cell), the cytotoxic protein is capable of causing death of the cell. Cell kill may be accomplished using a cytotoxic protein of the invention under varied conditions of target cells, such as an ex vivo manipulated target cell, a target cell cultured in vitro, a target cell within a tissue sample cultured in vitro, or a target cell in vivo.
B. Selective Cytotoxicity among Cell Types
[186] By targeting the delivery of enzymatically active, de-immunized, Shiga toxin regions using high-affinity binding regions to specific cell types, this potent cell-kill activity can be restricted to preferentially killing selected cell types.
[187] In certain embodiments, upon administration of the protein of the invention to a mixture of cell types, the protein is capable of selectively killing those cells which are physically coupled with an extracellular target biomolecule compared to cell types not physically coupled with an extracellular target biomolecule. Because members of the Shiga toxin family are adapted for killing eukaryotic cells, cytotoxic proteins designed using Shiga toxin effector regions can show potent cytotoxic activity. By targeting the delivery of enzymatically active Shiga toxin regions to specific cell types using high-affinity binding regions, this potent cell kill activity can be restricted to killing only those cell types desired to be targeted by their physical association with a target biomolecule of the chosen binding regions.
[188] In certain embodiments, the cytotoxic protein of the invention is capable of selectively or preferentially causing the death of a specific cell type within a mixture of two or more different cell types. This enables the targeted cytotoxic activity to specific cell types with a high preferentiality, such as a 3 -fold cytotoxic effect, over "bystander" cell types that do not express the target biomolecule. Alternatively, the expression of the target biomolecule of the binding region may be non-exclusive to one cell type if the target biomolecule is expressed in low enough amounts and/or physically coupled in low amounts with cell types that are not to be targeted. This enables the targeted cell-killing of specific cell types with a high preferentiality, such as a 3 -fold cytotoxic effect, over "bystander" cell types that do not express significant amounts of the target biomolecule or are not physically coupled to significant amounts of the target biomolecule.
[189] In certain further embodiments, upon administration of the cytotoxic protein to two different populations of cell types, the cytotoxic protein is capable of causing cell death as defined by the half-maximal cytotoxic concentration (CD50) on a population of target cells, whose members express an extracellular target biomolecule of the binding region of the cytotoxic protein, at a dose at least three-times lower than the CD50 dose of the same cytotoxic protein to a population of cells whose members do not express an extracellular target biomolecule of the binding region of the cytotoxic protein.
[1 0] In certain embodiments, the cytotoxic activity toward populations of cell types physically coupled with an extracellular target biomolecule is at least 3- fold higher than the cytotoxic activity toward populations of cell types not physically coupled with any extracellular target biomolecule of the binding region. According to the present invention, selective cytotoxicity may be quantified in terms of the ratio (a/b) of (a) cytotoxicity towards a population of cells of a specific cell type physically coupled with a target biomolecule of the binding region to (b) cytotoxicity towards a population of cells of a cell type not physically coupled with a target biomolecule of the binding region. In certain embodiments, the cytotoxicity ratio is indicative of selective cytotoxicity which is at least 3-fold, 5-fold, 10-fold, 15-fold, 20-fold, 25-fold, 30-fold, 40-fold, 50- fold, 75-fold, 100-fold, 250-fold, 500-fold, 750-fold, or 1000-fold higher for populations of cells or cell types physically coupled with a target biomolecule of the binding region compared to populations of cells or cell types not physically coupled with a target biomolecule of the binding region. [191] This preferential cell-killing function allows a targeted cell to be killed by certain cytotoxic proteins of the invention under varied conditions and in the presence of non-targeted bystander cells, such as ex vivo manipulated mixtures of cell types, in vitro cultured tissues with mixtures of cell types, or in vivo in the presence of multiple cell types (e.g. in situ or in its native location within a multicellular organism).
C. Delivery of Additional Exogenous Material into the Interior of Targeted Cells
[1 2] In addition to cytotoxic and cytostatic applications, proteins of the invention optionally may be used for information gathering and diagnostic functions. Futher, non-toxic variants of the cytotoxic proteins of the invention, or optionally toxic variants, may be used to deliver additional exogenous materials to and/or label the interiors of cells physically coupled with an extracellular target biomolecule of the cytotoxic protein. Various types of cells and/or cell populations which express target biomolecules to at least one cellular surface may be targeted by the proteins of the invention for receiving exogenous materials. The functional components of the present invention are modular, in that various Shiga toxin effector regions and additional exogenous materials may be linked to various binding regions to provide diverse applications, such as noninvasive in vivo imaging of tumor cells.
[193] Because the proteins of the invention, including nontoxic forms thereof, are capable of entering cells physically coupled with an extracellular target biomolecule recognized by its binding region, certain embodiments of the proteins of the invention may be used to deliver additional exogenous materials into the interior of targeted cell types. In one sense, the entire protein of the invention is an exogenous material which will enter the cell; thus, the
"additional" exogenous materials are heterologous materials linked to but other than the core cytotoxic protein itself. De-immunized Shiga toxin effector regions which become non-toxic after epitope disruption may still be useful for delivering exogenous materials into cells (e.g. R179A).
[194] "Additional exogenous material" as used herein refers to one or more molecules, often not generally present within a native target cell, where the proteins of the present invention can be used to specifically transport such material to the interior of a cell. Non-limiting examples of additional exogenous materials are peptides, polypeptides, proteins, polynucleotides, small molecule chemotherapeutic agents, and detection promoting agents.
[195] In certain embodiments, the additional exogenous material comprises a protein or polypeptide comprising an enzyme. In certain other embodiments, the additional exogenous material is a nucleic acid, such as, e.g. a ribonucleic acid that functions as a small inhibiting RNA (siRNA) or microRNA (miRNA). In certain embodiments, the additional exogenous material is an antigen, such as antigens derived from bacterial proteins, viral proteins, proteins mutated in cancer, proteins aberrantly expressed in cancer, or T-cell complementary determining regions. For example, exogenous materials include antigens, such as those characteristic of antigen-presenting cells infected by bacteria, and T-cell complementary determining regions capable of functioning as exogenous antigens. Additional examples of exogenous materials include polypeptides and proteins larger than an antigenic peptide, such as enzymes. Exogenous materials comprising polypeptides or proteins may optionally comprise one or more antigens whether known or unknown to the skilled worker.
D. Information Gathering for Diagnostic Functions
[196] Certain proteins of the invention have uses in the in vitro and/or in vivo detection of specific cells, cell types, and/or cell populations. In certain embodiments, the proteins described herein are used for both diagnosis and treatment, or for diagnosis alone. When the same cytotoxic protein is used for both diagnosis and treatment, the cytotoxic protein variant which incorporates a detection promoting agent for diagnosis may be rendered nontoxic by catalytic inactivation of a Shiga toxin effector region via one or more amino acid substitutions, including exemplary substitutions described herein. Nontoxic forms of the cytotoxic proteins of the invention that are conjugated to detection promoting agents optionally may be used for diagnostic functions, such as for companion diagnostics used in conjunction with a therapeutic regimen comprising the same or a related binding region.
[197] The ability to conjugate detection promoting agents known in the art to various proteins of the invention provides useful compositions for the detection of cancer, tumor, immune, and infected cells. These diagnostic embodiments of the proteins of the invention may be used for information gathering via various imaging techniques and assays known in the art. For example, diagnostic embodiments of the proteins of the invention may be used for information gathering via imaging of intracellular organelles (e.g. endocytotic, Golgi, endoplasmic reticulum, and cytosolic compartments) of individual cancer cells, immune cells, or infected cells in a patient or biopsy sample.
[198] Various types of information may be gathered using the diagnostic embodiments of the proteins of the invention whether for diagnostic uses or other uses. This information may be useful, for example, in diagnosing neoplastic cell types, determining therapeutic susceptibilities of a patient's disease, assaying the progression of antineoplastic therapies over time, assaying the progression of immunomodulatory therapies over time, assaying the progression of antimicrobial therapies over time, evaluating the presence of infected cells in transplantation materials, evaluating the presence of unwanted cell types in transplantation materials, and/or evaluating the presence of residual tumor cells after surgical excision of a tumor mass.
[199] For example, subpopulations of patients might be ascertained using information gathered using the diagnostic variants of the proteins of the invention, and then individual patients could be categorized into subpopulations based on their unique characteristic(s) revealed using those diagnostic embodiments. For example, the effectiveness of specific pharmaceuticals or therapies might be one type of criterion used to define a patient subpopulation. For example, a nontoxic diagnostic variant of a particular cytotoxic protein of the invention may be used to differentiate which patients are in a class or subpopulation of patients predicted to respond positively to a cytotoxic variant of the same protein of the invention. Accordingly, associated methods for patient identification, patient stratification, and diagnosis using de-immunized proteins of the invention, including non-toxic variants of cytotoxic proteins of the invention, are considered to be within the scope of the present invention.
E. Immunization/V accination Materials and Anti-Toxins
[200] The polypeptides of the invention have uses as biased immunization and/or vaccination materials for driving the elicitation of immune responses to specific epitopes in the presence of a de-immunized Shiga toxin effector region polypeptide of the invention. Infections by Shiga toxin producing
microorganisms are responsible for morbidity and mortality (Johannes, Nat Rev Microbiol 8: 105-16 (2010)). Shiga toxin producing bacteria are the leading cause of hemolytic uremic syndrome (HUS) and Shigellosis, as well as the associated conditions such as hemorrhagic colitis and diarrhea (see Karmali M, Mol Biotechnol 26: 1 17-22 (2004)). In addition, Shiga toxins are classified by the U.S. Centers for Disease Control and Prevention (CDC) as category B biothreat agents for their potential to be used as a bioweapon.
[201] Mammalian antibodies elicited during immune responses to a Shiga holotoxin or Shiga toxin subunit may be either neutralizing or non-neutralizing depending on the epitope. Furthermore, antibodies recognizing Shiga toxins may have different neutralizing effects depending on which Shiga toxin subunit comprises the epitope of the antibody (Krautz-Peterson G et al, Infect Immun 76: 1931-9 (2008)). Certain polypeptides of the invention are thus useful in methods to artificially drive mammalian immune responses away from certain epitope regions, such as, e.g., which elicit undesirable non-neutralizing antibodies and towards other epitopes, such as, e.g., which elicit desirable neutralizing and/or protective antibodies.
[202] Certain polypeptides of the invention have uses as biased immunization and/or vaccination materials in methods for reducing and/or eliminating the antigenicity and/or immunogenicity of specific epitopes while permitting the elicitation of immune responses to undisrupted, native epitopes. Immunization techniques for mammals may be used to generate anti-Shiga toxin antibodies which are biased away from a selected epitope region(s) of a Shiga toxin A Subunit.
[203] In addition, certain polypeptides of the invention may be used in various screening methods, such as, e.g., protein display screening and in vitro selections, for generation, identification, and affinity maturation of various binding domains, such as, e.g., immunoglobulin-type domains, which bind Shiga toxins such that screen selections are biased away from a selected epitope region(s) of a Shiga toxin A Subunit (see G15ckler J et al, Molecules 15: 2478- 90 (2010); Bradbury A et al, Nat Biotechnol 29: 245-54 (2011); Chen T, Keating A, Protein Sci 21 : 949-63 (2012); Geyer C et al, Methods Mol Biol 901 : 1 1-32 (2012)). These methods are particularly useful for targeting discontinuous epitopes which cannot be targeted in the absence of other untargeted epitopes. These methods are used to generate novel neutralizing antibodies and non- immunoglobulin type domains which inhibit Shiga toxin toxicity (see Perera L et al, J Clin Microbiol 26: 2127-31 (1988); Mukherjee J et al, Infect Immun 70: 5896-9 (2002); Smith M et al, Infect Immun 77: 2730-40 (2009); Rocha L et al, Toxins 4: 729-47 (2012); Tremblay J et al, Infect Immun 81: 4592-603 (2013); Skinner C et al, PLoS One 9: e99854 (2014)).
[204] Certain polypeptides of the invention may be used as immunization materials in methods for the creation and/or production of biased anti-Shiga toxin antibodies or anti-toxins. Immunization techniques for mammals may be used to generate anti-Shiga toxin antibodies which are biased away from a selected epitope region(s) of a Shiga toxin A Subunit. For example, certain polypeptides of the invention may be used as an immunization material to generate anti-Shiga toxin A Subunit antibodies which are biased away from a selected epitope region(s) of a Shiga toxin A Subunit. In addition, by combining a de-immunized Shiga toxin A Subunit of the invention with Shiga toxin B Subunits, immunization techniques may be used to generate anti-Shiga toxin antibodies biased toward epitopes present on native Shiga toxin B Subunits and/or interfaces between the Shiga toxin subunits present in the holotoxin. These anti-Shiga toxin antibodies have uses in methods involving immunodetection assays and for the creation of Shiga toxin neutralizing antibodies or anti-toxins (see Mukherjee J et al, Infect Immun 70: 5896-9 (2002); Sheoran A et al, Infect Immun 71 : 3125-30 (2003); Cheng L et al, Toxins 5: 1845-58 (2013); He X et al., J Immunol Methods 389: 18-28 (2013); Tremblay J et al, Infect Immun 81 : 4592-603 (2013)). Therefore, certain polypeptides of the invention may be used to better generate Shiga toxin neutralizing antibodies which then may be administered as a protective agent, therapeutic agent, or engineered into a protective and/or therapeutic for the treatment of infections by Shiga toxin producing microorganisms or other exposures to Shiga toxins (see Fujii J et al, Microb Pathog 25: 139-46 (1998); Mukherjee J et al, Infect Immun 70: 5896-9 (2002); Sheoran A et al., Infect Immun 71: 3125-30 (2003); Gao X et al, Vaccine 29: 6656-63 (2011); Cheng L et al, Toxins 5: 1845-58 (2013); He X et al, J Immunol Methods 389: 18-28 (2013); Tremblay J et al, Infect Immun 81: 4592-603 (2013); Vance D et al, J Biol Chem 288: 36538-47 (2013)). [205] Certain polypeptides of the invention may be used as vaccination materials in methods for the creation and/or production of biased anti-Shiga toxin antibodies. Vaccination techniques may be used with compositions comprising certain polypeptides of the invention to confer a mammal with active immunity to a future infection by a Shiga toxin producing microorganism or other exposure to a Shiga toxin (see Bosworth B et al., Infect Immun 64: 55-60 (1996); Rabinovitz B et al., J Dairy Sci 95: 3318-26 (2012)). Vaccine design may take into account the differences between epitopes that elicit neutralizing antibodies versus non-neutralizing antibodies with the possibility of non- neutralizing antibodies interfering with protective, neutralizing antibodies in a subject.
[206] For example, in a study of five antibodies to a Shiga holotoxin, only one showed neutralizing activity and this one bound both the A and B Subunits (He X et al, J Immunol Methods 389: 18-28 (2013)). Similarly for the AB toxin ricin, a neutralizing antibody recognizes an interface between the A and B
Subunits and prevents the liberation of an A Subunit fragment (O'Hara J, Mantis N, J Immunol Methods 395: 71-8 (2013)).
[207] For vaccination purposes, it might be more favorable to bias vaccine materials to elicit antibody responses primarily to external epitopes and/or epitopes which span interfaces of the A Subunit with the B Subunit in a holotoxin structure (O'Hara J, Mantis N, J Immunol Methods 395: 71-8 (2013); O'Hara J et al., Curr Top Microbiol Immunol 357: 209-41 (2012)). For example, vaccinations to ricin may have benefited from the elimination of a native immunogenic region that elicits only non-protective, non-neutralizing antibodies (Olsnes S, Toxicon 44: 361-70 (2004)). Similarly, the removal of an immunodominant region of ricin might have biased antibody responses away from producing non-neutralizing antibodies to certain epitopes (O'Hara J et al, Vaccine 28: 7035-46 (2010)) or even away from producing toxin-enhancing antibodies (Maddaloni M et al, J Immunol 172: 6221-8 (2004)). To that end, the elimination of certain epitopes within isolated regions of Shiga toxin A could remove undesired epitopes and drive antibody creation of more desirable epitopes, such as epitopes spanning Shiga toxin subunit interfaces.
[208] The polypeptides of the invention useful as biased immunization and/or vaccination materials may benefit from reductions and/or eliminations of Shiga toxin effector functions, such as enzymatic activity and/or cytotoxicity (He X et al, J Immunol Methods 389: 18-28 (2013); Skinner C et al, PLoS One 9: e99854 (2014)). Reduction or elimination of a Shiga toxin effector function may be accomplished by using one or more truncations and/or amino acid substitutions known to the skilled worker or discovered by the skilled worker using well- known methods. In addition, reduction or elimination of a Shiga toxin effector function may be accomplished by using the substitutions described in the Examples which exhibited attenuated, severely reduced, and/or loss of activity in a Shiga toxin effector assay, such as, e.g., ribosome inhibition and targeted cytotoxicity.
V. Variations in the Polypeptide Sequence of the De-Immunized Shiga Toxin Effector Region Polypeptides and Proteins
[209] The skilled worker will recognize that variations may be made to de- immunized Shiga toxin effector region polypeptides and proteins of the invention, and polynucleotides encoding any of the former, without diminishing their biological activities, e.g., by maintaining the overall structure and function of the toxin effector region in conjunction with one or more epitope disruptions which reduce antigenic and/or immunogenic potential. For example, some modifications may facilitate expression, purification, and/or pharmacokinetic properties, and/or immunogenicity. Such modifications are well known to the skilled worker and include, for example, a methionine added at the amino terminus to provide an initiation site, additional amino acids placed on either terminus to create conveniently located restriction sites or termination codons, and biochemical affinity tags fused to either terminus to provide for convenient detection and/or purification.
[210] Also contemplated herein is the inclusion of additional amino acid residues at the amino and/or carboxy termini, such as sequences for epitope tags or other moieties. The additional amino acid residues may be used for various purposes including, e.g., facilitating cloning, facilitating expression, post- translational modification, facilitating synthesis, purification, facilitating detection, and administration. Non-limiting examples of epitope tags and moieties are chitin binding protein domains, enteropeptidase cleavage sites, Factor Xa cleavage sites, FIAsH tags, FLAG tags, green fluorescent proteins (GFP), glutathione-S-transferase moieties, HA tags, maltose binding protein domains, myc tags, polyhistidine tags, ReAsH tags, strep-tags, strep-tag II, TEV protease sites, thioredoxin domans, thrombin cleavage site, and V5 epitope tags.
[21 1] In certain of the above embodiments, the polypeptide sequence of the de- immunized Shiga toxin effector region polypeptides and/or proteins of the invention are varied by one or more conservative amino acid substitutions introduced into the polypeptide region(s) as long as at least one amino acid is disrupted in at least one natively positioned epitope region provided herein. As used herein, the term "conservative substitution" denotes that one or more amino acids are replaced by another, biologically similar amino acid residue. Examples include substitution of amino acid residues with similar characteristics, e.g. small amino acids, acidic amino acids, polar amino acids, basic amino acids, hydrophobic amino acids and aromatic amino acids (see, for example, Table B, infra). An example of a conservative substitution with a residue normally not found in endogenous, mammalian peptides and proteins is the conservative substitution of an arginine or lysine residue with, for example, ornithine, canavanine, aminoethylcysteine, or another basic amino acid. For further information concerning phenotypically silent substitutions in peptides and proteins see, e.g., Bowie J et al, Science 247: 1306-10 (1990).
TABLE B. Examples of Conservative Amino Acid Substitutions
Figure imgf000082_0001
[212] In the conservative substitution scheme in Table B, exemplary conservative substitutions of amino acids are grouped by physicochemical properties - 1: neutral, hydrophilic; II: acids and amides; III: basic; IV: hydrophobic; V: aromatic, bulky amino acids, VI hydrophilic uncharged, VII aliphatic uncharged, VIII non-polar uncharged, IX cycloalkenyl-associated, X hydrophobic, XI polar, XII small, XIII turn-permitting, and XIV flexible. For example, conservative amino acid substitutions include the following: 1) S may be substituted for C; 2) M or L may be substituted for F; 3) Y may be substituted for M; 4) Q or E may be substituted for K; 5) N or Q may be substituted for H; and 6) H may be substituted for N.
[213] Additional conservative amino acid substitutions include the following: 1) S may be substituted for C; 2) M or L may be substituted for F; 3) Y may be substituted for M; 4) Q or E may be substituted for K; 5) N or Q may be substituted for H; and 6) H may be substituted for N.
[214] In certain embodiments, the de-immunized Shiga toxin effector region polypeptides and/or proteins of the invention may comprise functional fragments or variants of a polypeptide region of the invention that have, at most, 20, 15, 10, 9, 8, 7, 6, 5, 4, 3, 2, or 1 amino acid substitutions compared to a polypeptide sequence recited herein, as long as it retains a disruption of at least one amino acid in a natively positioned epitope region provided in the Examples (Tables 1, 2, 3, 4, and/or 5) and as long as it exhibits a significant level of a Shiga toxin effector function alone and/or as a component of a therapeutic and/or diagnostic composition. Variants of the de-immunized Shiga toxin effector region polypeptides and/or proteins of the invention are within the scope of the invention as a result of changing a polypeptide of the protein of the invention by altering one or more amino acids or deleting or inserting one or more amino acids, such as within the binding region or the Shiga toxin effector region, in order to achieve desired properties, such as changed cytotoxicity, changed cytostatic effects, changed immunogenicity, and/or changed serum half-life. A de-immunized Shiga toxin effector region polypeptide and/or a polypeptide of a protein of the invention may further be with or without a signal sequence.
[215] In certain embodiments, the de-immunized Shiga toxin effector region polypeptides and/or proteins of the invention shares at least 85%, 90%, 95%, 96%, 97%, 98%, 99% or more amino acid sequence identity to any one of the amino acid sequences of a protein recited herein, as long as it retains a disruption of at least one amino acid in a natively positioned epitope region provided in the Examples (Tables 1, 2, 3, 4, and/or 5) and measurable biological activity, such as cytotoxicity, extracellular target biomolecule binding, enzymatic catalysis, subcellular routing, or catalytically inactivating ribosomes.
[216] In certain embodiments, the de-immunized Shiga toxin effector region polypeptides and/or proteins of the invention may be altered to change the enzymatic activity and/or cytotoxicity of the Shiga toxin effector region as long as at least one amino acid is disrupted in a natively positioned epitope region provided in the Examples (Tables 1, 2, 3, 4, and/or 5). This change may or may not result in a change in the cytotoxicity of the Shiga toxin effector region polypeptide or cytotoxic protein of which the altered Shiga toxin effector region is a component. Possible alterations include mutations to the Shiga toxin effector region polypeptide selected from the group consisting of: a truncation, deletion, inversion, insertion and substitution as long as at least one amino acid is disrupted in a natively positioned epitope region provided in the Examples (Tables 1, 2, 3, 4, and/or 5).
[217] The cytotoxicity of the A Subunits of members of the Shiga toxin family may be reduced or eliminated by mutation or truncation. The positions labeled tyrosine-77, glutamate-167, arginine-170, tyrosine- 114, and tryptophan-203 have been shown to be important for the catalytic activity of Stx, Stxl, and Stx2 (Hovde C et al, Proc Natl Acad Sci USA 85: 2568-72 (1988); Deresiewicz R et al, Biochemistry 31 : 3272-80 (1992); Deresiewicz R et al, Mol Gen Genet 241 : 467-73 (1993); Ohmura M et al, Microb Pathog 15: 169-76 (1993); Cao C et al, Microbiol Immunol 38: 441-7 (1994); Suhan M, Hovde C, Infect Immun 66: 5252-9 (1998)). Mutating both glutamate-167 and arginine-170 eliminated the enzymatic activity of Slt-I Al in a cell-free ribosome inactivation assay
(LaPointe, J Biol Chem 280: 23310-18 (2005)). In another approach using de novo expression of Slt-I Al in the endoplasmic reticulum, mutating both glutamate-167 and arginine-170 eliminated Slt-I Al fragment cytotoxicity at that expression level (LaPointe, J Biol Chem 280: 23310-18 (2005)). A truncation analysis demonstrated that a fragment of StxA from residues 75 to 268 still retains significant enzymatic activity in vitro (Haddad, J Bacteriol 175: 4970-8 (1993)). A truncated fragment of Slt-I Al containing residues 1-239 displayed significant enzymatic activity in vitro and cytotoxicity by de novo expression in the cytosol (LaPointe, J Biol Chem 280: 23310-18 (2005)). Expression of a Slt-I Al fragment truncated to residues 1-239 in the endoplasmic reticulum was not cytotoxic because it could not retrotranslocate to the cytosol (LaPointe, J Biol Chem 280: 23310-18 (2005)).
[218] The most critical residues for enzymatic activity and/or cytotoxicity in the Shiga toxin A Subunits were mapped to the following residue-positions: asparagine-75, tyrosine-77, tyrosine- 1 14, glutamate-167, arginine- 170, arginine- 176, and tryptophan-203 among others (Di, Toxicon 57: 535-39 (2011)). In particular, a double-mutant construct of Stx2A containing glutamate-E167-to- lysine and arginine- 176-to-lysine mutations was completely inactivated;
whereas, many single mutations in Stxl and Stx2 showed a 10-fold reduction in cytotoxicity. Further, truncation of StxlA to 1-239 or 1-240 reduced its cytotoxicity, and similarly, truncation of Stx2A to a conserved hydrophobic residue reduced its cytotoxicity. The most critical residues for binding eukaryotic ribosomes and/or eukaryotic ribosome inhibition in the Shiga toxin A Subunit have been mapped to the following residue-positions: arginine-172, arginine-176, arginine-179, arginine-188, tyrosine-189, valine-191, and leucine- 233 among others (McCluskey A et al, PLoS One 7: e31 191 (2012).
[219] Shiga-like toxin 1 A Subunit truncations are catalytically active, capable of enzymatically inactivating ribosomes in vitro, and cytotoxic when expressed within a cell (LaPointe, J Biol Chem 280: 23310-18 (2005)). The smallest Shiga toxin A Subunit fragment exhibiting full enzymatic activity is a polypeptide composed of residues 1-239 of SltlA (LaPointe, J Biol Chem 280: 23310-18 (2005)). Although the smallest fragment of the Shiga toxin A Subunit reported to retain substantial catalytic activity was residues 75-247 of StxA (Al-Jaufy, Infect Immun 62: 956-60 (1994)), a StxA truncation expressed de novo within a eukaryotic cell requires only up to residue 240 to reach the cytosol and exert catalytic inactivation of ribosomes (LaPointe, J Biol Chem 280: 23310-18 (2005)).
[220] In certain embodiments of the de-immunized Shiga toxin effector region polypeptides and/or proteins of the invention derived from SLT-1A (SEQ ID NO: 1) or StxA (SEQ ID NO:2), these changes include substitution of the asparagine at position 75, tyrosine at position 77, tyrosine at position 1 14, glutamate at position 167, arginine at position 170, arginine at position 176, and/or substitution of the tryptophan at position 203. Examples of such substitutions will be known to the skilled worker based on the prior art, such as asparagine at position 75 to alanine, tyrosine at position 77 to serine, substitution of the tyrosine at position 1 14 to serine, substitution of the glutamate at position 167 to glutamate, substitution of the arginine at position 170 to alanine, substitution of the arginine at position 176 to lysine, and/or substitution of the tryptophan at position 203 to alanine. Other mutations which either enhance or reduce Shiga toxin enzymatic activity and/or cytotoxicity are within the scope of the invention and may be determined using well known techniques and assays disclosed herein.
[221] The de-immunized Shiga toxin effector region polypeptides and/or proteins of the invention may optionally be conjugated to one or more additional agents which may include therapeutic and/or diagnostic agents known in the art, including such agents as described herein.
VI. Production. Manufacture, and Purification of a De-Immunized Shiga Toxin Effector Region Polypeptide or Protein
[222] The de-immunized Shiga toxin effector region polypeptides and proteins of the invention may be produced using biochemical engineering techniques well known to those of skill in the art. For example, Shiga toxin effector region polypeptides and proteins of the invention may be manufactured by standard synthetic methods, by use of recombinant expression systems, or by any other suitable method. Thus, Shiga toxin effector region polypeptides and proteins of the invention may be synthesized in a number of ways, including, e.g. methods comprising: (1) synthesizing a polypeptide or polypeptide component of a protein using standard solid-phase or liquid-phase methodology, either stepwise or by fragment assembly, and isolating and purifying the final peptide compound product; (2) expressing a polynucleotide that encodes a polypeptide or polypeptide component of a protein of the invention in a host cell and recovering the expression product from the host cell or host cell culture; or (3) cell-free in vitro expression of a polynucleotide encoding a polypeptide or polypeptide component of a protein of the invention, and recovering the expression product; or by any combination of the methods of (1), (2) or (3) to obtain fragments of the peptide component, subsequently joining (e.g. ligating) the fragments to obtain the peptide component, and recovering the peptide component. [223] It may be preferable to synthesize a de-immunized Shiga toxin effector region polypeptide or a polypeptide or polypeptide component of a protein of the invention by means of solid-phase or liquid-phase peptide synthesis. Shiga toxin effector region polypeptides and proteins of the invention may suitably be manufactured by standard synthetic methods. Thus, peptides may be synthesized by, e.g. methods comprising synthesizing the peptide by standard solid-phase or liquid-phase methodology, either stepwise or by fragment assembly, and isolating and purifying the final peptide product. In this context, reference may be made to WO 1998/1 1125 or, inter alia, Fields G et al, Principles and Practice of Solid-Phase Peptide Synthesis (Synthetic Peptides, Grant G, ed., Oxford University Press, U.K., 2nd ed., 2002) and the synthesis examples therein.
[224] De-immunized Shiga toxin effector region polypeptides and proteins of the invention may be prepared (produced and purified) using recombinant techniques well known in the art. In general, methods for preparing
polypeptides by culturing host cells transformed or transfected with a vector comprising the encoding polynucleotide and recovering the polypeptide from cell culture are described in, e.g. Sambrook J et al, Molecular Cloning: A Laboratory Manual (Cold Spring Harbor Laboratory Press, NY, U.S., 1989); Dieffenbach C et al, PCR Primer: A Laboratory Manual (Cold Spring Harbor Laboratory Press, N.Y., U.S., 1995). Any suitable host cell may be used to produce a Shiga toxin effector region polypeptide and/or protein of the invention. Host cells may be cells stably or transiently transfected, transformed, transduced or infected with one or more expression vectors which drive expression of a polypeptide of the invention. In addition, a Shiga toxin effector region polypeptide and/or protein of the invention may be produced by modifying the polynucleotide encoding a polypeptide or protein of the invention that result in altering one or more amino acids or deleting or inserting one or more amino acids in order to achieve desired properties, such as changed cytotoxicity, changed cytostatic effects, changed immunogenicity, and/or changed serum half-life.
[225] There are a wide variety of expression systems which may be chosen to produce a protein of the invention. For example, host organisms for expression of proteins of the invention include prokaryotes, such as E. coli and B. subtilis, eukaryotic cells, such as yeast and filamentous fungi (like S. cerevisiae, P.
pastoris, A. awamori, and K. lactis), algae (like C. reinhardtii), insect cell lines, mammalian cells (like CHO cells), plant cell lines, and eukaryotic organisms such as transgenic plants (like A. thaliana and N. benthamiana).
[226] Accordingly, the present invention also provides methods for producing de-immunized Shiga toxin effector region polypeptides and/or proteins of the invention according to above recited methods and using a polynucleotide encoding part or all of a polypeptide of the invention or a polypeptide component of a protein of the invention, an expression vector comprising at least one polynucleotide of the invention capable of encoding part or all of a polypeptide of the invention when introduced into a host cell, and/or a host cell comprising a polynucleotide or expression vector of the invention.
[227] When a polypeptide or protein is expressed using recombinant techniques in a host cell or cell-free system, it is advantageous to separate (or purify) the desired polypeptide or protein away from other components, such as host cell factors, in order to obtain preparations that are of high purity or are substantially homogeneous. Purification can be accomplished by methods well known in the art, such as centrifugation techniques, extraction techniques, chromatographic and fractionation techniques (e.g. size separation by gel filtration, charge separation by ion-exchange column, hydrophobic interaction chromatography, reverse phase chromatography, chromatography on silica or cation-exchange resins such as DEAE and the like, chromatofocusing, and Protein A Sepharose chromatography to remove contaminants), and precipitation techniques (e.g. ethanol precipitation or ammonium sulfate precipitation). Any number of biochemical purification techniques may be used to increase the purity of a Shiga toxin effector region polypeptide and/or protein of the invention. In certain embodiments, the polypeptides and proteins of the invention may optionally be purified in homo-multimeric forms (i.e. a protein complex of two or more identical polypeptides or proteins of the invention).
[228] In the Examples below are descriptions of non-limiting examples of methods for producing a protein of the invention, as well as specific but non- limiting aspects of production for exemplary proteins of the invention. VII. Pharmaceutical and Diagnostic Compositions Comprising a De-Immunized Shiga Toxin Effector Region Polypeptide or Protein
[229] The present invention provides polypeptides and proteins for use, alone or in combination with one or more additional therapeutic agents, in a pharmaceutical composition, for treatment or prophylaxis of conditions, diseases, disorders, or symptoms described in further detail below (e.g. cancers, malignant tumors, non-malignant tumors, growth abnormalities, immune disorders, and microbial infections). The present invention further provides pharmaceutical compositions comprising a polypeptide or protein of the invention, or a pharmaceutically acceptable salt or solvate thereof, according to the invention, together with at least one pharmaceutically acceptable carrier, excipient, or vehicle. In certain embodiments, the pharmaceutical composition of the invention may comprise homo-multimeric and/or hetero-multimeric forms of the polypeptides or proteins of the invention. The pharmaceutical compositions will be useful in methods of treating, ameliorating, or preventing a disease, condition, disorder, or symptom described in further detail below. Each such disease, condition, disorder, or symptom is envisioned to be a separate embodiment with respect to uses of a pharmaceutical composition according to the invention. The invention further provides pharmaceutical compositions for use in at least one method of treatment according to the invention, as described in more detail below.
[230] As used herein, the terms "patient" and "subject" are used
interchangeably to refer to any organism, commonly vertebrates such as humans and animals, which presents symptoms, signs, and/or indications of at least one disease, disorder, or condition. These terms include mammals such as the non- limiting examples of primates, livestock animals (e.g. cattle, horses, pigs, sheep, goats, etc.), companion animals (e.g. cats, dogs, etc.) and laboratory animals (e.g. mice, rabbits, rats, etc.).
[231] As used herein, "treat," "treating," or "treatment" and grammatical variants thereof refer to an approach for obtaining beneficial or desired clinical results. The terms may refer to slowing the onset or rate of development of a condition, disorder or disease, reducing or alleviating symptoms associated with it, generating a complete or partial regression of the condition, or some combination of any of the above. For the purposes of this invention, beneficial or desired clinical results include, but are not limited to, reduction or alleviation of symptoms, diminishment of extent of disease, stabilization (e.g. not worsening) of state of disease, delay or slowing of disease progression, amelioration or palliation of the disease state, and remission (whether partial or total), whether detectable or undetectable. "Treat," "treating," or "treatment" can also mean prolonging survival relative to expected survival time if not receiving treatment. A subject (e.g. a human) in need of treatment may thus be a subject already afflicted with the disease or disorder in question. The terms "treat," "treating," or "treatment" includes inhibition or reduction of an increase in severity of a pathological state or symptoms relative to the absence of treatment, and is not necessarily meant to imply complete cessation of the relevant disease, disorder, or condition. With regard to tumors and/or cancers, treatment includes reduction in overall tumor burden and/or individual tumor size.
[232] As used herein, the terms "prevent," "preventing," "prevention" and grammatical variants thereof refer to an approach for preventing the
development of, or altering the pathology of, a condition, disease, or disorder. Accordingly, "prevention" may refer to prophylactic or preventive measures. For the purposes of this invention, beneficial or desired clinical results include, but are not limited to, prevention or slowing of symptoms, progression or development of a disease, whether detectable or undetectable. A subject (e.g. a human) in need of prevention may thus be a subject not yet afflicted with the disease or disorder in question. The term "prevention" includes slowing the onset of disease relative to the absence of treatment, and is not necessarily meant to imply permanent prevention of the relevant disease, disorder or condition.
Thus "preventing" or "prevention" of a condition may in certain contexts refer to reducing the risk of developing the condition, or preventing or delaying the development of symptoms associated with the condition.
[233] As used herein, an "effective amount" or "therapeutically effective amount" is an amount or dose of a composition (e.g. a therapeutic composition or agent) that produces at least one desired therapeutic effect in a subject, such as preventing or treating a target condition or beneficially alleviating a symptom associated with the condition. The most desirable therapeutically effective amount is an amount that will produce a desired efficacy of a particular treatment selected by one of skill in the art for a given subject in need thereof. This amount will vary depending upon a variety of factors understood by the skilled worker, including but not limited to the characteristics of the therapeutic compound (including activity, pharmacokinetics, pharmacodynamics, and bioavailability), the physiological condition of the subject (including age, sex, disease type, disease stage, general physical condition, responsiveness to a given dosage, and type of medication), the nature of the pharmaceutically acceptable carrier or carriers in the formulation, and the route of administration. One skilled in the clinical and pharmacological arts will be able to determine a therapeutically effective amount through routine experimentation, namely by monitoring a subject's response to administration of a compound and adjusting the dosage accordingly (see e.g. Remington: The Science and Practice of Pharmacy (Gennaro A, ed., Mack Publishing Co., Easton, PA, U.S., 19th ed., 1995)).
[234] Diagnostic compositions comprise a polypeptide or protein of the invention and one or more detection promoting agents. Various detection promoting agents are known in the art, such as isotopes, dyes, colorimetric agents, contrast enhancing agents, fluorescent agents, bioluminescent agents, and magnetic agents. These agents may be incorporated into the polypeptide or protein of the invention at any position. The incorporation of the agent may be via an amino acid residue(s) of the cytotoxic protein or via some type of linkage known in the art, including via linkers and/or chelators. The incorporation of the agent is in such a way to enable the detection of the presence of the diagnostic composition in a screen, assay, diagnostic procedure, and/or imaging technique.
[235] When producing or manufacturing a diagnostic composition of the invention, a protein of the invention may be directly or indirectly linked to one or more detection promoting agents. There are numerous detection promoting agents known to the skilled worker which can be operably linked to the polypeptides or proteins of the invention for information gathering methods, such as for diagnostic and/or prognostic applications to diseases, disorders, or conditions of an organism (see e.g. Cai W et al, JNucl Med 48: 304-10 (2007); Nayak T, Brechbiel M, Bioconjug Chem 20: 825-41 (2009); Paudyal P et al, Oncol Rep 22: 115-9 (2009); Qiao J et al., PLoS ONE 6: el8103 (2011); Sano K et al, Breast Cancer Res 14: R61 (2012)). For example, detection promoting agents include image enhancing contrast agents, such as fluorescent dyes (e.g. Alexa680, indocyanine green, and Cy5.5), isotopes and radionuclides, such as nC, 13N, 150, 18F, 32P, 51Mn, 52mMn, 52Fe, 55Co, 62Cu, 64Cu,67Cu, 67Ga, 68Ga, 72As, 73Se, 75Br, 76Br, 82mRb, 83Sr, 86Y, 90Y, 89Zr, 94mTc, 94Tc, "mTc, 110In, mIn, 120I, 123I, 1241, 125I, 131I, 154Gd, 155Gd, 156Gd, 157Gd, 158Gd, 177Lu, 186Re, 188Re, and 223R; paramagnetic ions, such as chromium (III), manganese (II), iron (III), iron (II), cobalt (II), nickel (II), copper (II), neodymium (III), samarium (III), ytterbium (III), gadolinium (III), vanadium (II), terbium (III), dysprosium (III), holmium (III) or erbium (III); metals, such as lanthanum (III), gold (III), lead (II), and bismuth (III); ultrasound-contrast enhancing agents, such as liposomes; radiopaque agents, such as barium, gallium, and thallium compounds. Detection promoting agents may be incorporated directly or indirectly by using an intermediary functional group, such as chelators like 2-benzyl DTPA, PAMAM, NOTA, DOTA, TETA, analogs thereof, and functional equivalents of any of the foregoing (see Leyton J et al, Clin Cancer Res 14: 7488-96 (2008)).
[236] There are numerous standard techniques known to the skilled worker for incorporating, affixing, and/or conjugating various detection promoting agents to proteins, especially to immunoglobulins and immunoglobulin-derived domains (Wu A, Methods 65: 139-47 (2014)). Similarly, there are numerous imaging approaches known to the skilled worker, such as non-invasive in vivo imaging techniques commonly used in the medical arena, for example: computed tomography imaging (CT scanning), optical imaging (including direct, fluorescent, and bioluminescent imaging), magnetic resonance imaging (MRI), positron emission tomography (PET), single-photon emission computed tomography (SPECT), ultrasound, and x-ray computed tomography imaging (see Kaur S et al, Cancer Lett 315: 97-111 (2012), for review).
Production or Manufacture of a Pharmaceutical and/or Diagnostic Composition Comprising a De-Immunized Shiga Toxin Effector Region Polypeptide or Protein
[237] Pharmaceutically acceptable salts or solvates of any of the polypeptides and proteins of the invention are likewise within the scope of the present invention. [238] The term "solvate" in the context of the present invention refers to a complex of defined stoichiometry formed between a solute (in casu, a polypeptide compound or pharmaceutically acceptable salt thereof according to the invention) and a solvent. The solvent in this connection may, for example, be water, ethanol or another pharmaceutically acceptable, typically small-molecular organic species, such as, but not limited to, acetic acid or lactic acid. When the solvent in question is water, such a solvate is normally referred to as a hydrate.
[239] Polypeptides and proteins of the present invention, or salts thereof, may be formulated as pharmaceutical compositions prepared for storage or administration, which typically comprise a therapeutically effective amount of a compound of the invention, or a salt thereof, in a pharmaceutically acceptable carrier. The term "pharmaceutically acceptable carrier" includes any of the standard pharmaceutical carriers. Pharmaceutically acceptable carriers for therapeutic use are well known in the pharmaceutical art, and are described, for example, in Remington 's Pharmaceutical Sciences (Mack Publishing Co. (A. Gennaro, ed., 1985). As used herein, "pharmaceutically acceptable carrier" includes any and all physiologically acceptable, i.e. compatible, solvents, dispersion media, coatings, antimicrobial agents, isotonic, and absorption delaying agents, and the like. Pharmaceutically acceptable carriers or diluents include those used in formulations suitable for oral, rectal, nasal or parenteral (including subcutaneous, intramuscular, intravenous, intradermal, and transdermal) administration. Exemplary pharmaceutically acceptable carriers include sterile aqueous solutions or dispersions and sterile powders for the extemporaneous preparation of sterile injectable solutions or dispersions.
Examples of suitable aqueous and nonaqueous carriers that may be employed in the pharmaceutical compositions of the invention include water, ethanol, polyols (such as glycerol, propylene glycol, polyethylene glycol, and the like), and suitable mixtures thereof, vegetable oils, such as olive oil, and injectable organic esters, such as ethyloleate. Proper fluidity can be maintained, for example, by the use of coating materials, such as lecithin, by the maintenance of the required particle size in the case of dispersions, and by the use of surfactants. In certain embodiments, the carrier is suitable for intravenous, intramuscular,
subcutaneous, parenteral, spinal or epidermal administration (e.g. by injection or infusion). Depending on selected route of administration, the cytotoxic protein or other pharmaceutical component may be coated in a material intended to protect the compound from the action of low pH and other natural inactivating conditions to which the active cytotoxic protein may encounter when administered to a patient by a particular route of administration.
[240] The formulations of the pharmaceutical compositions of the invention may conveniently be presented in unit dosage form and may be prepared by any of the methods well known in the art of pharmacy. In such form, the composition is divided into unit doses containing appropriate quantities of the active component. The unit dosage form can be a packaged preparation, the package containing discrete quantities of the preparations, for example, packeted tablets, capsules, and powders in vials or ampoules. The unit dosage form can also be a capsule, cachet, or tablet itself, or it can be the appropriate number of any of these packaged forms. It may be provided in single dose injectable form, for example in the form of a pen. Compositions may be formulated for any suitable route and means of administration. Subcutaneous or transdermal modes of administration may be particularly suitable for therapeutic proteins described herein.
[241] The pharmaceutical compositions of the invention may also contain adjuvants such as preservatives, wetting agents, emulsifying agents and dispersing agents. Preventing the presence of microorganisms may be ensured both by sterilization procedures, and by the inclusion of various antibacterial and antifungal agents, for example, paraben, chlorobutanol, phenol sorbic acid, and the like. Isotonic agents, such as sugars, sodium chloride, and the like into the compositions, may also be desirable. In addition, prolonged absorption of the injectable pharmaceutical form may be brought about by the inclusion of agents which delay absorption such as, aluminum monostearate and gelatin.
[242] A pharmaceutical composition of the invention also optionally includes a pharmaceutically acceptable antioxidant. Exemplary pharmaceutically acceptable antioxidants are water soluble antioxidants such as ascorbic acid, cysteine hydrochloride, sodium bisulfate, sodium metabisulfite, sodium sulfite and the like; oil-soluble antioxidants, such as ascorbyl palmitate, butylated hydroxyanisole (BHA), butylated hydroxytoluene (BHT), lecithin, propylgallate, alpha-tocopherol, and the like; and metal chelating agents, such as citric acid, ethylenediamine tetraacetic acid (EDTA), sorbitol, tartaric acid, phosphoric acid, and the like.
[243] In another aspect, the present invention provides pharmaceutical compositions comprising one or a combination of different polypeptides and/or proteins of the invention, or an ester, salt or amide of any of the foregoing, and at least one pharmaceutically acceptable carrier.
[244] Therapeutic compositions are typically sterile and stable under the conditions of manufacture and storage. The composition may be formulated as a solution, microemulsion, liposome, or other ordered structure suitable to high drug concentration. The carrier may be a solvent or dispersion medium containing, for example, water, alcohol such as ethanol, polyol (e.g. glycerol, propylene glycol, and liquid polyethylene glycol), or any suitable mixtures. The proper fluidity may be maintained, for example, by the use of a coating such as lecithin, by the maintenance of the required particle size in the case of dispersion and by use of surfactants according to formulation chemistry well known in the art. In certain embodiments, isotonic agents, e.g. sugars, polyalcohols such as mannitol, sorbitol, or sodium chloride may be desirable in the composition. Prolonged absorption of injectable compositions may be brought about by including in the composition an agent that delays absorption for example, monostearate salts and gelatin.
[245] Solutions or suspensions used for intradermal or subcutaneous application typically include one or more of: a sterile diluent such as water for injection, saline solution, fixed oils, polyethylene glycols, glycerine, propylene glycol or other synthetic solvents; antibacterial agents such as benzyl alcohol or methyl parabens; antioxidants such as ascorbic acid or sodium bisulfite;
chelating agents such as ethylenediaminetetraacetic acid; buffers such as acetates, citrates or phosphates; and tonicity adjusting agents such as, e.g., sodium chloride or dextrose. The pH can be adjusted with acids or bases, such as hydrochloric acid or sodium hydroxide, or buffers with citrate, phosphate, acetate and the like. Such preparations may be enclosed in ampoules, disposable syringes or multiple dose vials made of glass or plastic.
[246] Sterile injectable solutions may be prepared by incorporating a polypeptide or protein of the invention in the required amount in an appropriate solvent with one or a combination of ingredients described above, as required, followed by sterilization microfiltration. Dispersions may be prepared by incorporating the active compound into a sterile vehicle that contains a dispersion medium and other ingredients, such as those described above. In the case of sterile powders for the preparation of sterile injectable solutions, the methods of preparation are vacuum drying and freeze-drying (lyophilization) that yield a powder of the active ingredient in addition to any additional desired ingredient from a sterile-filtered solution thereof.
[247] When a therapeutically effective amount of a polypeptide or protein of the invention is designed to be administered by, e.g. intravenous, cutaneous or subcutaneous injection, the binding agent will be in the form of a pyrogen-free, parenterally acceptable aqueous solution. Methods for preparing parenterally acceptable protein solutions, taking into consideration appropriate pH, isotonicity, stability, and the like, are within the skill in the art. A preferred pharmaceutical composition for intravenous, cutaneous, or subcutaneous injection will contain, in addition to binding agents, an isotonic vehicle such as sodium chloride injection, Ringer's injection, dextrose injection, dextrose and sodium chloride injection, lactated Ringer's injection, or other vehicle as known in the art. A pharmaceutical composition of the present invention may also contain stabilizers, preservatives, buffers, antioxidants, or other additives well known to those of skill in the art.
[248] As described elsewhere herein, a polypeptide or protein of the invention may be prepared with carriers that will protect the compound against rapid release, such as a controlled release formulation, including implants, transdermal patches, and microencapsulated delivery systems. Biodegradable, biocompatible polymers can be used, such as ethylene vinyl acetate, polyanhydrides, polyglycolic acid, collagen, polyorthoesters, and polylactic acid. Many methods for the preparation of such formulations are patented or generally known to those skilled in the art (see e.g. Sustained and Controlled Release Drug Delivery Systems (Robinson J, ed., Marcel Dekker, Inc., NY, U.S., 1978)).
[249] In certain embodiments, the pharmaceutical composition of the invention may be formulated to ensure a desired distribution in vivo. For example, the blood-brain barrier excludes many large and/or hydrophilic compounds. To target a therapeutic compound or composition of the invention to a particular in vivo location, they can be formulated, for example, in liposomes which may comprise one or more moieties that are selectively transported into specific cells or organs, thus enhancing targeted drug delivery. Exemplary targeting moieties include folate or biotin; mannosides; antibodies; surfactant protein A receptor; pl20 catenin and the like.
[250] Pharmaceutical compositions include parenteral formulations designed to be used as implants or particulate systems. Examples of implants are depot formulations composed of polymeric or hydrophobic components such as emulsions, ion exchange resins, and soluble salt solutions. Examples of particulate systems are microspheres, microparticles, nanocapsules, nanospheres, and nanoparticles (see e.g. Honda M et al, Int J Nanomedicine 8: 495-503 (2013); Sharma A et al, Biomed Res Int 2013 : 960821 (2013); Ramishetti S, Huang L, Ther Deliv 3 : 1429-45 (2012)). Controlled release formulations may be prepared using polymers sensitive to ions, such as, e.g. liposomes, polaxamer 407, and hydroxyapatite.
VIII. Polynucleotides, Expression Vectors, and Host Cells
[251] Beyond the polypeptides and proteins of the present invention, the polynucleotides which encode the polypeptides and proteins of the invention, or functional portions thereof, are within the scope of the present invention. The term "polynucleotide" is equivalent to the term "nucleic acids" both of which include polymers of deoxyribonucleic acids (DNAs), polymers of ribonucleic acids (RNAs), analogs of these DNAs or RNAs generated using nucleotide analogs, and derivatives, fragments and homologs thereof. The polynucleotide of the invention may be single-, double-, or triple-stranded. Disclosed polynucleotides are specifically disclosed to include all polynucleotides capable of encoding an exemplary cytotoxic protein, for example, taking into account the wobble known to be tolerated in the third position of RNA codons, yet encoding for the same amino acid as a different RNA codon (see Stothard P,
Biotechniques 28: 1 102-4 (2000)).
[252] In one aspect, the invention provides polynucleotides which encode a de- immunized Shiga toxin effector region polypeptide and/or a protein of the invention, or a fragment or derivative thereof. The polynucleotides may include, e.g., nucleic acid sequence encoding a polypeptide at least 50%, 55% , 60% , 65%, 70%, 75%, 80%, 85%, 90%, 95%, 99% or more, identical to a polypeptide comprising one of the amino acid sequences of the protein. The invention also includes polynucleotides comprising nucleotide sequences that hybridize under stringent conditions to a polynucleotide which encodes de-immunized Shiga toxin effector region polypeptide and/or a protein of the invention, or a fragment or derivative thereof, or the antisense or complement of any such sequence.
[253] Derivatives or analogs of the polynucleotides (or de-immunized Shiga toxin effector region polypeptides and/or proteins) of the invention include, inter alia, polynucleotide (or polypeptide) molecules having regions that are substantially homologous to the polynucleotides, de-immunized Shiga toxin effector region polypeptides, or proteins of the invention, e.g. by at least about 45%, 50%, 70%, 80%, 95%, 98%, or even 99% identity (with a preferred identity of 80-99%) over a polynucleotide or polypeptide sequence of the same size or when compared to an aligned sequence in which the alignment is done by a computer homology program known in the art. An exemplary program is the GAP program (Wisconsin Sequence Analysis Package, Version 8 for UNIX,
Genetics Computer Group, University Research Park, Madison, WI, U.S.) using the default settings, which uses the algorithm of Smith T, Waterman M, Adv. Appl. Math. 2: 482-9 (1981). Also included are polynucleotides capable of hybridizing to the complement of a sequence encoding the proteins of the invention under stringent conditions (see e.g. Ausubel F et al, Current Protocols in Molecular Biology (John Wiley & Sons, New York, NY, U.S., 1993)), and below. Stringent conditions are known to those skilled in the art and may be found in Current Protocols in Molecular Biology (John Wiley & Sons, NY, U.S., Ch. Sec. 6.3.1-6.3.6 (1989)).
[254] The present invention further provides expression vectors that comprise the polynucleotides within the scope of the invention. The polynucleotides capable of encoding the de-immunized Shiga toxin effector region polypeptides and/or proteins of the invention may be inserted into known vectors, including bacterial plasmids, viral vectors and phage vectors, using material and methods well known in the art to produce expression vectors. Such expression vectors will include the polynucleotides necessary to support production of contemplated Shiga toxin effector region polypeptides and/or proteins of the invention within any host cell of choice or cell-free expression systems (e.g. pTxbl and pIVEX2.3 described in the Examples below). The specific polynucleotides comprising expression vectors for use with specific types of host cells or cell- free expression systems are well known to one of ordinary skill in the art, can be determined using routine experimentation, or may be purchased.
[255] The term "expression vector," as used herein, refers to a polynucleotide, linear or circular, comprising one or more expression units. The term
"expression unit" denotes a polynucleotide segment encoding a polypeptide of interest and capable of providing expression of the nucleic acid segment in a host cell. An expression unit typically comprises a transcription promoter, an open reading frame encoding the polypeptide of interest, and a transcription terminator, all in operable configuration. An expression vector contains one or more expression units. Thus, in the context of the present invention, an expression vector encoding a Shiga toxin effector region polypeptide and/or a protein comprising a single polypeptide chain (e.g. a scFv genetically recombined with a Shiga toxin effector region) includes at least an expression unit for the single polypeptide chain, whereas a protein comprising, e.g. two or more polypeptide chains (e.g. one chain comprising a VL domain and a second chain comprising a VH domain linked to a toxin effector region) includes at least two expression units, one for each of the two polypeptide chains of the protein. For expression of multi-chain proteins of the invention, an expression unit for each polypeptide chain may also be separately contained on different expression vectors (e.g. expression may be achieved with a single host cell into which expression vectors for each polypeptide chain has been introduced).
[256] Expression vectors capable of directing transient or stable expression of polypeptides and proteins are well known in the art. The expression vectors generally include, but are not limited to, one or more of the following: a heterologous signal sequence or peptide, an origin of replication, one or more marker genes, an enhancer element, a promoter, and a transcription termination sequence, each of which is well known in the art. Optional regulatory control sequences, integration sequences, and useful markers that can be employed are known in the art.
[257] The term "host cell" refers to a cell which can support the replication or expression of the expression vector. Host cells may be prokaryotic cells, such as E. coli or eukaryotic cells (e.g. yeast, insect, amphibian, bird, or mammalian cells). Creation and isolation of host cell lines comprising a polynucleotide of the invention or capable of producing a polypeptide and/or protein of the invention can be accomplished using standard techniques known in the art.
[258] De-immunized Shiga toxin effector region polypeptides and/or proteins within the scope of the present invention may be variants or derivatives of the polypeptides and proteins described herein that are produced by modifying the polynucleotide encoding a polypeptide and/or protein by altering one or more amino acids or deleting or inserting one or more amino acids that may render it more suitable to achieve desired properties, such as more optimal expression by a host cell.
IX. Delivery Devices and Kits
[259] In certain embodiments, the invention relates to a device comprising one or more compositions of matter of the invention, such as a pharmaceutical composition, for delivery to a subject. Thus, a delivery device comprising one or more compounds of the invention can be used to administer to a patient a composition of matter of the invention by various delivery methods, including: intravenous, subcutaneous, intramuscular or intraperitoneal injection; oral administration; transdermal administration; pulmonary or transmucosal administration; administration by implant, osmotic pump, cartridge or micro pump; or by other means recognized by a person of skill in the art.
[260] Also within the scope of the invention are kits comprising at least one composition of matter of the invention, and optionally, packaging and instructions for use. Kits may be useful for drug administration and/or diagnostic information gathering. A kit of the invention may optionally comprise at least one additional reagent (e.g., standards, markers and the like). Kits typically include a label indicating the intended use of the contents of the kit. The kit may further comprise reagents and other tools for detecting a cell type (e.g. tumor cell) in a sample or in a subject, or for diagnosing whether a patient belongs to a group that responds to a therapeutic strategy which makes use of a compound, composition or related method of the invention as described herein. X. Methods for Using a De-Immunized Shiga Toxin Effector Region
Polypeptide or Protein or a Pharmaceutical and/or Diagnostic Composition Thereof
[261] Generally, it is an object of the invention to provide pharmacologically active agents, as well as compositions comprising the same, that can be used in the prevention and/or treatment of diseases, disorders, and conditions, such as certain cancers, tumors, growth abnormalities, immune disorders, or further pathological conditions mentioned herein. Accordingly, the present invention provides methods of using the polypeptides, proteins, and pharmaceutical compositions of the invention for the targeted killing of cells, for delivering additional exogenous materials into targeted cells, for labeling of the interiors of targeted cells, for collecting diagnostic information, and for treating diseases, disorders, and conditions as described herein.
[262] In particular, it is an object of the invention to provide such
pharmacologically active agents, compositions, and/or methods that have certain advantages compared to the agents, compositions, and/or methods that are currently known in the art. Accordingly, the present invention provides methods of using polypeptides and proteins with specified polypeptide sequences and pharmaceutical compositions thereof. For example, any of the polypeptide sequences in SEQ ID NOs: 4-59 may be specifically utilized as a component of the protein used in the following methods.
[263] The present invention provides methods of killing a cell comprising the step of contacting the cell, either in vitro or in vivo, with a polypeptide, protein, or pharmaceutical composition of the present invention. The polypeptides, proteins, and pharmaceutical compositions of the invention can be used to kill a specific cell type upon contacting a cell or cells with one of the claimed compositions of matter. In certain embodiments, a cytotoxic polypeptide, protein, or pharmaceutical composition of the present invention can be used to kill specific cell types in a mixture of different cell types, such as mixtures comprising cancer cells, infected cells, and/or hematological cells. In certain embodiments, a cytotoxic polypeptide, protein, or pharmaceutical composition of the present invention can be used to kill cancer cells in a mixture of different cell types. In certain embodiments, a cytotoxic polypeptide, protein, or pharmaceutical composition of the present invention can be used to kill specific cell types in a mixture of different cell types, such as pre-transplantation tissues. In certain embodiments, a polypeptide, protein, or pharmaceutical composition of the present invention can be used to kill specific cell types in a mixture of cell types, such as pre-administration tissue material for therapeutic purposes. In certain embodiments, a polypeptide, protein, or pharmaceutical composition of the present invention can be used to selectively kill cells infected by viruses or microorganisms, or otherwise selectively kill cells expressing a particular extracellular target biomolecule, such as a cell surface biomolecule. The polypeptides, proteins, and pharmaceutical compositions of the invention have varied applications, including, e.g., uses in depleting unwanted cell types from tissues either in vitro or in vivo, uses in modulating immune responses to treat graft versus host disease, uses as antiviral agents, uses as anti-parasitic agents, and uses in purging transplantation tissues of unwanted cell types.
[264] In certain embodiments, a cytotoxic polypeptide, protein, or
pharmaceutical composition of the present invention, alone or in combination with other compounds or pharmaceutical compositions, can show potent cell-kill activity when administered to a population of cells, in vitro or in vivo in a subject such as in a patient in need of treatment. By targeting the delivery of enzymatically active Shiga toxin regions using high-affinity binding regions to specific cell types, this potent cell-kill activity can be restricted to specifically and selectively kill certain cell types within an organism, such as certain cancer cells, neoplastic cells, malignant cells, non-malignant tumor cells, or infected cells.
[265] The present invention provides a method of killing a cell in a patient in need thereof, the method comprising the step of administering to the patient at least one cytotoxic polypeptide or protein of the present invention, or a pharmaceutical composition thereof.
[266] Certain embodiments of the cytotoxic polypeptide, protein, or pharmaceutical compositions thereof can be used to kill a cancer cell in a patient by targeting an extracellular biomolecule found physically coupled with a cancer or tumor cell. The terms "cancer cell" or "cancerous cell" refers to various neoplastic cells which grow and divide in an abnormally accelerated fashion and will be clear to the skilled person. The term "tumor cell" includes both malignant and non-malignant cells. Generally, cancers and/or tumors can be defined as diseases, disorders, or conditions that are amenable to treatment and/or prevention. The cancers and tumors (either malignant or non-malignant) which are comprised by cancer cells and/or tumor cells will be clear to the skilled person. Neoplastic cells are often associated with one or more of the following: unregulated growth, lack of differentiation, local tissue invasion, angiogenesis, and metastasis.
[267] Certain embodiments of the cytotoxic polypeptide or protein of the invention, or pharmaceutical compositions thereof, can be used to kill an immune cell (whether healthy or malignant) in a patient by targeting an extracellular biomolecule found physically coupled with an immune cell.
[268] Certain embodiments of the cytotoxic polypeptide or protein of the invention, or pharmaceutical compositions thereof, can be used to kill an infected cell in a patient by targeting an extracellular biomolecule found physically coupled with an infected cell.
[269] It is within the scope of the present invention to utilize the protein of the invention or pharmaceutical composition thereof for the purposes of purging patient cell populations (e.g. bone marrow) of malignant, neoplastic, or otherwise unwanted T-cells and/or B-cells and then reinfusing the T-cell and/or B-cells depleted material into the patient (see e.g. van Heeckeren W et al, Br J Haematol 132: 42-55 (2006); (see e.g. Alpdogan O, van den Brink M, Semin Oncol 39: 629-42 (2012)).
[270] It is within the scope of the present invention to utilize the protein of the invention or pharmaceutical composition thereof for the purposes of ex vivo depletion of T cells and/or B-cells from isolated cell populations removed from a patient. In one non-limiting example, the protein of the invention can be used in a method for prophylaxis of organ and/or tissue transplant rejection wherein the donor organ or tissue is perfused prior to transplant with a cytotoxic protein of the invention or a pharmaceutical composition thereof in order to purge the organ of donor T-cells and/or B-cells (see e.g. Alpdogan O, van den Brink M, Semin Oncol 39: 629-42 (2012)).
[271] It is also within the scope of the present invention to utilize the protein of the invention or pharmaceutical composition thereof for the purposes of depleting T-cells and/or B-cells from a donor cell population as a prophylaxis against graft-versus-host disease, and induction of tolerance, in a patient to undergo a bone marrow and or stem cell transplant (see e.g. van Heeckeren W et al, Br J Haematol 132: 42-55 (2006); (see e.g. Alpdogan O, van den Brink M, Semin Oncol 39: 629-42 (2012)).
[272] Certain embodiments of the cytotoxic polypeptide or protein of the invention, or pharmaceutical compositions thereof, can be used to kill an infected cell in a patient by targeting an extracellular biomolecule found physically coupled with an infected cell.
[273] Additionally, the present invention provides a method of treating a disease, disorder, or condition in a patient comprising the step of administering to a patient in need thereof a therapeutically effective amount of at least one of the cytotoxic polypeptide or protein of the invention, or a pharmaceutical composition thereof. Contemplated diseases, disorders, and conditions that can be treated using this method include cancers, malignant tumors, non-malignant tumors, growth abnormalities, immune disorders, and microbial infections. Administration of a "therapeutically effective dosage" of a compound of the invention can result in a decrease in severity of disease symptoms, an increase in frequency and duration of disease symptom-free periods, or a prevention of impairment or disability due to the disease affliction.
[274] The therapeutically effective amount of a compound of the present invention will depend on the route of administration, the type of mammal being treated, and the physical characteristics of the specific patient under
consideration. These factors and their relationship to determining this amount are well known to skilled practitioners in the medical arts. This amount and the method of administration can be tailored to achieve optimal efficacy, and may depend on such factors as weight, diet, concurrent medication and other factors, well known to those skilled in the medical arts. The dosage sizes and dosing regimen most appropriate for human use may be guided by the results obtained by the present invention, and may be confirmed in properly designed clinical trials. An effective dosage and treatment protocol may be determined by conventional means, starting with a low dose in laboratory animals and then increasing the dosage while monitoring the effects, and systematically varying the dosage regimen as well. Numerous factors may be taken into consideration by a clinician when determining an optimal dosage for a given subject. Such considerations are known to the skilled person. [275] An acceptable route of administration may refer to any administration pathway known in the art, including but not limited to aerosol, enteral, nasal, ophthalmic, oral, parenteral, rectal, vaginal, or transdermal (e.g. topical administration of a cream, gel or ointment, or by means of a transdermal patch). "Parenteral administration" is typically associated with injection at or in communication with the intended site of action, including infraorbital, infusion, intraarterial, intracapsular, intracardiac, intradermal, intramuscular,
intraperitoneal, intrapulmonary, intraspinal, intrasternal, intrathecal, intrauterine, intravenous, subarachnoid, subcapsular, subcutaneous, transmucosal, or transtracheal administration.
[276] For administration of a pharmaceutical composition of the invention, the dosage range will generally be from about 0.0001 to 100 milligrams per kilogram (mg/kg), and more, usually 0.01 to 5 mg/kg, of the host body weight. Exemplary dosages may be 0.25 mg/kg body weight, 1 mg/kg body weight, 3 mg/kg body weight, 5 mg/kg body weight or 10 mg/kg body weight or within the range of 1-10 mg/kg. An exemplary treatment regime is a once or twice daily administration, or a once or twice weekly administration, once every two weeks, once every three weeks, once every four weeks, once a month, once every two or three months or once every three to 6 months. Dosages may be selected and readjusted by the skilled health care professional as required to maximize therapeutic benefit for a particular patient.
[277] Pharmaceutical compositions of the invention will typically be administered to the same patient on multiple occasions. Intervals between single dosages can be, for example, 2-5 days, weekly, monthly, every two or three months, every six months, or yearly. Intervals between administrations can also be irregular, based on regulating blood levels or other markers in the subject or patient. Dosage regimens for a compound of the invention include intravenous administration of 1 mg/kg body weight or 3 mg/kg body weight with the compound administered every two to four weeks for six dosages, then every three months at 3 mg/kg body weight or 1 mg/kg body weight.
[278] A pharmaceutical composition of the present invention may be administered via one or more routes of administration, using one or more of a variety of methods known in the art. As will be appreciated by the skilled worker, the route and/or mode of administration will vary depending upon the desired results. Routes of administration for polypeptides, proteins, and pharmaceutical compositions of the invention include, e.g. intravenous, intramuscular, intradermal, intraperitoneal, subcutaneous, spinal, or other parenteral routes of administration, for example by injection or infusion. In other embodiments, a polypeptide, protein, or pharmaceutical composition of the invention may be administered by a non-parenteral route, such as a topical, epidermal or mucosal route of administration, for example, intranasally, orally, vaginally, rectally, sublingually, or topically.
[279] Therapeutic polypeptides, proteins, or pharmaceutical compositions of the invention may be administered with one or more of a variety of medical devices known in the art. For example, in one embodiment, a pharmaceutical composition of the invention may be administered with a needleless hypodermic injection device. Examples of well-known implants and modules useful in the present invention are in the art, including e.g., implantable micro-infusion pumps for controlled rate delivery; devices for administering through the skin; infusion pumps for delivery at a precise infusion rate; variable flow implantable infusion devices for continuous drug delivery; and osmotic drug delivery systems. These and other such implants, delivery systems, and modules are known to those skilled in the art.
[280] A polypeptide, protein, or pharmaceutical composition of the present invention may be administered alone or in combination with one or more other therapeutic or diagnostic agents. A combination therapy may include a cytotoxic protein of the invention or pharmaceutical composition thereof combined with at least one other therapeutic agent selected based on the particular patient, disease or condition to be treated. Examples of other such agents include, inter alia, a cytotoxic, anti-cancer or chemotherapeutic agent, an anti-inflammatory or antiproliferative agent, an antimicrobial or antiviral agent, growth factors, cytokines, an analgesic, a therapeutically active small molecule or polypeptide, a single chain antibody, a classical antibody or fragment thereof, or a nucleic acid molecule which modulates one or more signaling pathways, and similar modulating therapeutics which may complement or otherwise be beneficial in a therapeutic or prophylactic treatment regimen.
[281] Treatment of a patient with a polypeptide, protein, or pharmaceutical composition of the invention preferably leads to cell death of targeted cells and/or the inhibition of growth of targeted cells. As such, cytotoxic proteins of the invention, and pharmaceutical compositions comprising them, will be useful in methods for treating a variety of pathological disorders in which killing or depleting target cells may be beneficial, such as, inter alia, cancer, tumors, other growth abnormalities, immune disorders, and infected cells. The present invention provides methods for suppressing cell proliferation, and treating cell disorders, including neoplasia, overactive B-cells, and overactive T-cells.
[282] In certain embodiments, polypeptides, proteins, and pharmaceutical compositions of the invention can be used to treat or prevent cancers, tumors (malignant and non-malignant), growth abnormalities, immune disorders, and microbial infections. In a further aspect, the above ex vivo method can be combined with the above in vivo method to provide methods of treating or preventing rejection in bone marrow transplant recipients, and for achieving immunological tolerance.
[283] In certain embodiments, the present invention provides methods for treating malignancies or neoplasms and other blood cell associated cancers in a mammalian subject, such as a human, the method comprising the step of administering to a subject in need thereof a therapeutically effective amount of a cytotoxic protein or pharmaceutical composition of the invention.
[284] The cytotoxic polypeptides, proteins, and pharmaceutical compositions of the invention have varied applications, including, e.g., uses in removing unwanted T-cells, uses in modulating immune responses to treat graft-versus- host disease, uses as antiviral agents, uses as antimicrobial agents, and uses in purging transplantation tissues of unwanted cell types. The cytotoxic polypeptides, proteins, and pharmaceutical compositions of the present invention are commonly anti-neoplastic agents - meaning they are capable of treating and/or preventing the development, maturation, or spread of neoplastic or malignant cells by inhibiting the growth and/or causing the death of cancer or tumor cells.
[285] In certain embodiments, a polypeptide, protein, or pharmaceutical composition of the present invention is used to treat a B-cell-, plasma cell- or antibody- mediated disease or disorder, such as for example leukemia, lymphoma, myeloma, Human Immunodeficiency Virus-related diseases, amyloidosis, hemolytic uremic syndrome, polyarteritis, septic shock, Crohn's Disease, rheumatoid arthritis, ankylosing spondylitis, psoriatic arthritis, ulcerative colitis, psoriasis, asthma, Sjorgren's syndrome, graft-versus-host disease, graft rejection, diabetes, vasculitis, scleroderma, and systemic lupus erythematosus.
[286] In another aspect, certain embodiments of the polypeptides, proteins, and pharmaceutical compositions of the present invention are antimicrobial agents - meaning they are capable of treating and/or preventing the acquisition, development, or consequences of microbiological pathogenic infections, such as caused by viruses, bacteria, fungi, prions, or protozoans.
[287] It is within the scope of the present invention to provide a prophylaxis or treatment for diseases or conditions mediated by T-cells or B-cells by administering the cytotoxic protein or the invention, or a pharmaceutical composition thereof, to a patient for the purpose of killing T-cells or B-cells in the patient. This usage is compatible with preparing or conditioning a patient for bone marrow transplantation, stem cell transplantation, tissue transplantation, or organ transplantation, regardless of the source of the transplanted material, e.g. human or non-human sources.
[288] It is within the scope of the present invention to provide a bone marrow recipient for prophylaxis or treatment of host-versus-graft disease via the targeted cell-killing of host T-cells using a cytotoxic polypeptide, protein, or pharmaceutical composition of the present invention.
[289] The cytotoxic polypeptides, proteins, and pharmaceutical compositions of the present invention can be utilized in a method of treating cancer comprising administering to a patient, in need thereof, a therapeutically effective amount of a cytotoxic polypeptide, protein, or pharmaceutical composition of the present invention. In certain embodiments of the methods of the present invention, the cancer being treated is selected from the group consisting of: bone cancer (such as multiple myeloma or Ewing's sarcoma), breast cancer, central/peripheral nervous system cancer (such as brain cancer, neurofibromatosis, or
glioblastoma), gastrointestinal cancer (such as stomach cancer or colorectal cancer), germ cell cancer (such as ovarian cancers and testicular cancers, glandular cancer (such as pancreatic cancer, parathyroid cancer,
pheochromocytoma, salivary gland cancer, or thyroid cancer), head-neck cancer (such as nasopharyngeal cancer, oral cancer, or pharyngeal cancer), hematological cancers (such as leukemia, lymphoma, or myeloma), kidney- urinary tract cancer (such as renal cancer and bladder cancer), liver cancer, lung/pleura cancer (such as mesothelioma, small cell lung carcinoma, or non- small cell lung carcinoma), prostate cancer, sarcoma (such as angiosarcoma, fibrosarcoma, Kaposi's sarcoma, or synovial sarcoma), skin cancer (such as basal cell carcinoma, squamous cell carcinoma, or melanoma), and uterine cancer.
[290] The polypeptides, proteins, and pharmaceutical compositions of the present invention can be utilized in a method of treating an immune disorder comprising administering to a patient, in need thereof, a therapeutically effective amount of the cytotoxic protein or a pharmaceutical composition of the present invention. In certain embodiments of the methods of the present invention, the immune disorder is related to an inflammation associated with a disease selected from the group consisting of: amyloidosis, ankylosing spondylitis, asthma, Crohn's disease, diabetes, graft rejection, graft-versus-host disease, Hashimoto's thyroiditis, hemolytic uremic syndrome, HIV-related diseases, lupus erythematosus, multiple sclerosis, polyarteritis, psoriasis, psoriatic arthritis, rheumatoid arthritis, scleroderma, septic shock, Sjorgren's syndrome, ulcerative colitis, and vasculitis.
[291] Among certain embodiments of the present invention is using the polypeptide or protein of the invention as a component of a pharmaceutical composition or medicament for the treatment or prevention of a cancer, tumor, other growth abnormality, immune disorder, and/or microbial infection. For example, immune disorders presenting on the skin of a patient may be treated with such a medicament in efforts to reduce inflammation. In another example, skin tumors may be treated with such a medicament in efforts to reduce tumor size or eliminate the tumor completely.
[292] Beneficial clinical effects may be obtained by treatment regimens involving the sequential administration of multiple cytotoxic proteins of the invention to the same subject where each cytotoxic protein comprises a Shiga toxin effector region de-immunized in a different region in order to avoid or reduce the development of a prolonged immune response(s) to a single cytotoxic protein from treatment regimens involving serial administration of an identical therapeutic. [293] Certain cytotoxic polypeptides, proteins, and pharmaceutical compositions of the invention may be used in molecular neurosurgery applications such as immunolesioning and neuronal tracing (see, Wiley R, Lappi D, Adv Drug Deliv Rev 55: 1043-54 (2003), for review). For example, the targeting domain may be selected or derived from various ligands, such as neurotransmitters and neuropeptides, which target specific neuronal cell types by binding neuronal surface receptors, such as a neuronal circuit specific G-protein coupled receptor. Similarly, the targeting domain may be selected from or derived from antibodies that bind neuronal surface receptors. Because Shiga toxins robustly direct their own retrograde axonal transport, certain cytotoxic proteins of the invention may be used to kill a neuron(s) which expresses the extracellular target at a site of cytotoxic protein injection distant from the cell body (see Llewellyn-Smith I et al, JNeurosci Methods 103: 83-90 (2000)). These neuronal cell-type-specific -targeting cytotoxic polypeptides and proteins have uses in neuroscience research, such as for elucidating mechanisms of sensations (see e.g. Mishra S, Hoon M, Science 340: 968-71 (2013)), and creating model systems of neurodegenerative diseases, such as Parkinson's and Alzheimer's (see e.g. Hamlin A et al, PLoS One e53472 (2013)).
[294] Among certain embodiments of the present invention is a method of using a polypeptide, protein, pharmaceutical composition, and/or diagnostic composition of the invention to label or detect the interiors of neoplastic cells and/or immune cell types. Based on the ability of certain polypeptides, proteins, and pharmaceutical compositions of the invention to enter specific cell types and route within cells via retrograde intracellular transport, the interior compartments of specific cell types are labeled for detection. This can be performed on cells in situ within a patient or on cells and tissues removed from an organism, e.g. biopsy material.
[295] Among certain embodiment of the present invention is a method of using a polypeptide, protein, pharmaceutical composition, and/or diagnostic composition of the invention to detect the presence of a cell type for the purpose of information gathering regarding diseases, conditions and/or disorders. The method comprises contacting a cell with a diagnostically sufficient amount of a cytotoxic molecule to detect the cytotoxic molecule by an assay or diagnostic technique. The phrase "diagnostically sufficient amount" refers to an amount that provides adequate detection and accurate measurement for information gathering purposes by the particular assay or diagnostic technique utilized. Generally, the diagnostically sufficient amount for whole organism in vivo diagnostic use will be a non-cumulative dose of between 0.1 mg to 100 mg of the detection promoting agent linked protein of the invention per kg of subject per subject. Typically, the amount of polypeptide or protein of the invention used in these information gathering methods will be as low as possible provided that it is still a diagnostically sufficient amount. For example, for in vivo detection in an organism, the amount of polypeptide, protein, or pharmaceutical composition of the invention administered to a subject will be as low as feasibly possible.
[296] The cell-type specific targeting of polypeptides and proteins of the invention combined with detection promoting agents provides a way to detect and image cells physically coupled with an extracellular target biomolecule of a binding region of the molecule of the invention. Imaging of cells using the polypeptides or proteins of the invention may be performed in vitro or in vivo by any suitable technique known in the art. Diagnostic information may be collected using various methods known in the art, including whole body imaging of an organism or using ex vivo samples taken from an organism. The term "sample" used herein refers to any number of things, but not limited to, fluids such as blood, urine, serum, lymph, saliva, anal secretions, vaginal secretions, and semen, and tissues obtained by biopsy procedures. For example, various detection promoting agents may be utilized for non-invasive in vivo tumor imaging by techniques such as magnetic resonance imaging (MRI), optical methods (such as direct, fluorescent, and bioluminescent imaging), positron emission tomography (PET), single-photon emission computed tomography (SPECT), ultrasound, x-ray computed tomography, and combinations of the aforementioned (see, Kaur S et al, Cancer Lett 315: 97-1 11 (2012), for review).
[297] Among certain embodiments of the present invention is a method of using a polypeptide, protein, or pharmaceutical composition of the invention as a diagnostic composition to label or detect the interiors of cancer, tumor, and/or immune cell types (see e.g., Koyama Y et al, Clin Cancer Res 13 : 2936-45 (2007); Ogawa M et al, Cancer Res 69: 1268-72 (2009); Yang L et al, Small 5: 235-43 (2009)). Based on the ability of certain polypeptides, proteins, and pharmaceutical compositions of the invention to enter specific cell types and route within cells via retrograde intracellular transport, the interior compartments of specific cell types are labeled for detection. This can be performed on cells in situ within a patient or on cells and tissues removed from an organism, e.g. biopsy material.
[298] Diagnostic compositions of the invention may be used to characterize a disease, disorder, or condition as potentially treatable by a related
pharmaceutical composition of the invention. Certain compositions of matter of the invention may be used to determine whether a patient belongs to a group that responds to a therapeutic strategy which makes use of a compound, composition or related method of the invention as described herein or is well suited for using a delivery device of the invention.
[299] Diagnostic compositions of the invention may be used after a disease, e.g. a cancer, is detected in order to better characterize it, such as to monitor distant metastases, heterogeneity, and stage of cancer progression. The phenotypic assessment of disease disorder or infection can help prognostication and prediction during therapeutic decision making. In disease reoccurrence, certain methods of the invention may be used to discriminate localized versus systemic problems.
[300] Diagnostic compositions of the invention may be used to assess responses to therapeutic(s) regardless of the type of therapeutic, e.g. small molecule drug, biological drug, or cell-based therapy. For example, certain embodiments of the diagnostics of the invention may be used to measure changes in tumor size, changes in antigen positive cell populations including number and distribution, or monitoring a different marker than the antigen targeted by a therapy already being administered to a patient (see Smith- Jones P et al, Nat. Biotechnol 22: 701-6 (2004); Evans M et al, Proc. Natl. Acad. Sci. U.S.A. 108: 9578-82 (201 1)).
[301] Certain embodiments of the method used to detect the presence of a cell type may be used to gather information regarding diseases, disorders, and conditions, such as, for example bone cancer (such as multiple myeloma or Ewing's sarcoma), breast cancer, central/peripheral nervous system cancer (such as brain cancer, neurofibromatosis, or glioblastoma), gastrointestinal cancer (such as stomach cancer or colorectal cancer), germ cell cancer (such as ovarian cancers and testicular cancers, glandular cancer (such as pancreatic cancer, parathyroid cancer, pheochromocytoma, salivary gland cancer, or thyroid cancer), head-neck cancer (such as nasopharyngeal cancer, oral cancer, or pharyngeal cancer), hematological cancers (such as leukemia, lymphoma, or myeloma), kidney -urinary tract cancer (such as renal cancer and bladder cancer), liver cancer, lung/pleura cancer (such as mesothelioma, small cell lung carcinoma, or non-small cell lung carcinoma), prostate cancer, sarcoma (such as angiosarcoma, fibrosarcoma, Kaposi's sarcoma, or synovial sarcoma), skin cancer (such as basal cell carcinoma, squamous cell carcinoma, or melanoma), uterine cancer, AIDS, amyloidosis, ankylosing spondylitis, asthma, autism, cardiogenesis, Crohn's disease, diabetes, erythematosus, gastritis, graft rejection, graft- versus-host disease, Grave's disease, Hashimoto's thyroiditis, hemolytic uremic syndrome, HIV-related diseases, lupus erythematosus,
lymphoproliferative disorders, multiple sclerosis, myasthenia gravis, neuroinflammation, polyarteritis, psoriasis, psoriatic arthritis, rheumatoid arthritis, scleroderma, septic shock, Sjorgren's syndrome, systemic lupus erythematosus, ulcerative colitis, vasculitis, cell proliferation, inflammation, leukocyte activation, leukocyte adhesion, leukocyte chemotaxis, leukocyte maturation, leukocyte migration, neuronal differentiation, acute lymphoblastic leukemia (ALL), T acute lymphocytic leukemia/lymphoma (ALL), acute myelogenous leukemia, acute myeloid leukemia (AML), B-cell chronic lymphocytic leukemia (B-CLL), B-cell prolymphocytic lymphoma, Burkitt's lymphoma (BL), chronic lymphocytic leukemia (CLL), chronic myelogenous leukemia (CML-BP), chronic myeloid leukemia (CML), diffuse large B-cell lymphoma, follicular lymphoma, hairy cell leukemia (HCL), Hodgkin's Lymphoma (HL), intravascular large B-cell lymphoma, lymphomatoid granulomatosis, lymphoplasmacytic lymphoma, MALT lymphoma, mantle cell lymphoma, multiple myeloma (MM), natural killer cell leukemia, nodal marginal B-cell lymphoma, Non-Hodgkin's lymphoma (NHL), plasma cell leukemia, plasmacytoma, primary effusion lymphoma, pro-lymphocytic leukemia, promyelocytic leukemia, small lymphocytic lymphoma, splenic marginal zone lymphoma, T-cell lymphoma (TCL), heavy chain disease, monoclonal gammopathy, monoclonal immunoglobulin deposition disease, myelodusplastic syndromes (MDS), smoldering multiple myeloma, and Waldenstrom macroglobulinemia.
[302] In certain embodiments, the polypeptides and proteins of the invention, or pharmaceutical compositions thereof, are used for both diagnosis and treatment, or for diagnosis alone.
[303] The polypeptides of the invention have uses as immunization materials for eliciting immune responses to specific epitopes based on the presence of a disruption(s) in a selected epitope region(s). A polypeptide of the invention may be used as an immunization material for the administration to a mammal and/or used in a display screen to generate an immunoglobulin domain recognizing a Shiga toxin.
[304] The present invention is further illustrated by the following non-limiting examples of selectively cytotoxic proteins comprising de-immunized Shiga toxin effector regions derived from A Subunits of members of the Shiga toxin family and binding regions capable of binding extracellular target biomolecules physically coupled to specific cell types.
EXAMPLES
[305] The following examples demonstrate certain embodiments of the present invention. However, it is to be understood that these examples are for illustration purposes only and do not intend, nor should any be construed, to be wholly definitive as to conditions and scope of this invention. The experiments in the following examples were carried out using standard techniques, which are well known and routine to those of skill in the art, except where otherwise described in detail.
[306] In order to improve Shiga toxin-derived polypeptide regions for therapeutic and diagnostic applications in mammals, predicted B-cell epitopes throughout entire toxin effector regions were systematically disrupted with the goal of dampening mammalian B-cell mediated immune responses. Amino acid sequences representing A Subunits of multiple Shiga toxins were analyzed to identify putative antigenic and/or immunogenic epitopes. Computational tools were used to predict B-cell and T-cell epitopes, including considerations of publicly available protein database structural data. Epitope predictions were validated empirically. Various de-immunized Shiga toxin effector polypeptides were experimentally tested for loss of epitopes present in native Shiga toxin A Subunits and retention of Shiga toxin effector functions. The biological activities of exemplary de-immunized Shiga toxin effector polypeptides as components of various cytotoxic proteins were compared to cytotoxic proteins comprising non-de-immunized Shiga toxin effector polypeptides, referred to herein as "wild-type" or "WT."
[307] The following examples of de-immunized Shiga toxin effector polypeptides demonstrate the retention of Shiga toxin effector functions as components of various cytotoxic proteins. The exemplary cytotoxic proteins bound to target biomolecules expressed by targeted cell types and entered the targeted cells. The internalized cytotoxic proteins effectively routed their de- immunized Shiga toxin effector regions to the cytosol to inactivate ribosomes and subsequently caused the apoptotic death of the targeted cells similar to cytotoxic proteins comprising wild-type Shiga toxin effector regions.
Furthermore, the following examples demonstrate that multiple epitope disruptions can be combined in Shiga toxin effector region polypeptides to reduce the overall antigenicity and/or immunogenicity of a cytotoxic protein of the invention while retaining potent cytotoxicity. Example 1. Predicting Immunogenic and Antigenic Epitopes in Shiga Toxin A Subunits
[308] The antigenic and/or immunogenic sites within the A Subunits of Shiga toxins had never been systematically mapped. Computational methods were utilized to predict antigenic and/or immunogenic epitopes in various Shiga toxin A Subunits. Both B-cell epitopes and CD4+ T-cell epitopes with potential to elicit responses in mammalian immune systems were predicted in silico.
[309] Linear B-cell epitopes were predicted for the mature A Subunit of Shiga- like toxin 1 (SLT-1A; SEQ ID NO: l) from the polypeptide sequence and 3D structural data of Shiga-Like Toxin Chain A (PDB ID: 1DM0 A) by Prolmmune Inc. (Sarasota, FL, U.S.) using their REVEAL® system.
[310] In parallel, B-cell epitopes were predicted from the amino acid sequences of the A Subunits of Shiga toxin (StxA; SEQ ID NO:2), Shiga-like toxin 1 (SLT- 1A; SEQ ID NO: l), and Shiga-like toxin 2 (Stx2A; SEQ ID NO:3) using the BcePred webserver (Saha S, Raghava G, Lecture Notes in Comput Sci 3239: 197-204 (2004)), Bepipred Linear Epitope Prediction (Larsen J et al., Immunome Res 2: 2 (2006)), and ElliPro Antibody epitope prediction (Haste Andersen P et al, Protein Sci 15: 2558-67 (2006); Ponomarenko J, Bourne P, BMC Struct Biol 7: 64 (2007)). The various computational methods revealed similar predictions for B-cell epitope regions in the three prototypical Shiga toxin A Subunits (Tables 1-3).
Table 1. B-Cell Epitope Predictions for the Mature, Native A Subunit of
Shiga-like Toxin 1 (SEQ ID NO:l)
Figure imgf000116_0001
Table 2. B-Cell Epitope Predictions for the Mature, Native A Subunit of
Shiga Toxin (SEQ ID NO:2)
Figure imgf000116_0002
Table 3. B-Cell Epitope Predictions for the Mature, Native A Subunit of Shiga-like Toxin 2 (SEQ ID NO:3)
Figure imgf000117_0001
[31 1] Previous sequence alignment studies predicted immune epitope regions in Shiga toxin A Subunits which might be antigenic and/or immunogenic based on an epitope in ricin bound by a neutralizing antibody (Lebeda F, Olson M, Int J Biol Macromol 24: 19-26 (1999); Zemla A, Ecale Zhou C, Bioinform Biol Insights 2: 5-13 (2008)). It was predicted that there might be a conserved immunogenic epitope in StxA around residues 90-107 and in Stx2A around residues 1 12-129 (Zemla A, Ecale Zhou C, Bioinform Biol Insights 2: 5-13 (2008)). However, this prediction was admittedly unreliable due to key differences between the plant toxin ricin and the bacterial Shiga toxins, such as, e.g., the large amount of sequence variability between ricin and Shiga toxins, the lack of a N-terminal alpha helix in the A subunits of Shiga toxins, and the predicted region is shorter and less solvent-exposed in Shiga toxins compared to ricin ((Fraser M et al, Nature Struct Biol 1 : 59 (1994); Lebeda F, Olson M, Int J Biol Macromol 24: 19-26 (1999); Zemla A, Ecale Zhou C, Bioinform Biol Insights !: 5-13 (2008)).
[312] The Immune Epitope Database (IEDB) curated by the National Institutes of Allergy and Infectious Diseases of the U.S. (NIAID) is said to provide all experimentally characterized B- and T-cell epitopes of Shiga toxins. Currently, the IEDB provides only a single epitope for only a single Shiga toxin A Subunit (Stx2dA): IEDB identification number 1 10493, an experimentally determined, discontinuous B-cell epitope comprising amino acids 42-49, 96-100, and 245- 260 (Smith M et al, Infect Immun 77: 2730-40 (2009)).
[313] The nine predicted B-cell epitope regions identified by more than one method in SLT-IA (Table 4) were disrupted in the following Examples.
Table 4. Nine Putative B-Cell Epitope Regions Shared by Prototypical
Shiga toxin A Subunits
Figure imgf000118_0001
[314] In addition, Shiga toxin A Subunits were analyzed using the Epitopia webserver for predicting B-cell epitopes and immunogenic residues (Rubinstein N et al, BMC Bioinformatics 10: 287 (2009)). Epitopia was used to identify linear amino acid residue regions predicted to be immunogenic in SLT-IA based on an Epitopia score of 4 or 5 ("high") for the majority of amino acid residues in a linear amino acid residue stretch. The Epitopia analysis predicted an immunogenic region occurs from amino acid residues 1 to 15 in SLT-IA (designated as Epitope Region 0 below, see Table 5, infra). Based on the Epitopia analysis, the immunogenic epitope region 2 in SLT-IA (see Table 4) might include position 49. Based on the Epitopia analysis, the immunogenic epitope region 3 in SLT-IA (see Table 4) might include position 53 and extend to around position 62-66 (designated as Epitope Region 3* below, see Table 5, infra), the Epitope Region 4 in SLT-IA (see Table 4) might include position 94 (designated as Epitope Region 4* below, see Table 5, infra), and the epitope region 6 in SLT-IA (see Table 4) might start at position 179 and extend to around position 188-190 (designated as Epitope Region 6* below, see Table 5, infra). Note the starred B-cell epitope regions all completely encompass their respective overlapping region with the same numerical identifier.
[315] These ten epitope regions (#0-9) were compared for overlap with predicted CD4+ T-cell epitopes. T-cell epitopes were predicted for the mature A
Subunit of Shiga-like toxin 1 (SEQ ID NO: 1) by the REVEAL™
Immunogenicity System (IS) T-cell assay performed by Prolmmune Inc.
(Sarasota, FL, U.S.). This assay uses multiple overlapping peptide sequences from the subject protein to test for the elicitation of any immune response by CD4+ T-cells from healthy donor cell samples depleted of CD8+ T-cells. Of the
13 predicted B-cell epitope regions, all of them overlapped with at least one predicted CD4+ T-cell epitope (Table 5). All the predicted B-cell epitope regions in Table 5 were disrupted or deleted individually or in combination in the following Examples.
Table 5. Predicted B-Cell Epitope Regions with Overlapping Predicted
CD4+ T-Cell Epitopes
Figure imgf000119_0001
Example 2. De-Immunization of Shiga Toxin Effector Polypeptides
[316] Deletions and/or amino acid substitutions were made in the putative B- cell and T-cell epitopes of Shiga toxin effector polypeptides derived from the A Subunit of Shiga-like Toxin 1 (SLT-1A). In addition to the described point mutations that disrupted predicted epitopes, some constructs comprised one or more point mutations that had no apparent effect on Shiga toxin effector enzymatic activity or cytotoxicity, such as, e.g., R223A in SLT-1A, C242S in SLT-1A, and/or C261 S in SLT-1A.
[317] In this example, a Shiga toxin effector polypeptide region was derived from the A Subunit of Shiga-like Toxin 1 (SLT-1A). A polynucleotide that encoded amino acids 1-251 of SLT-1A was used as a template to create various polynucleotides encoding various Shiga toxin effector polypeptides with one or more disruptions of a predicted B-cell epitope(s). Shiga toxin effector polypeptides comprising one or more epitope disruptions were expressed from these polynucleotides to explore which disruptions might most effectively de- immunize various Shiga toxin effector polypeptides in the context of a cytotoxic protein of the invention.
[318] Truncating the carboxy -terminus of SLT- 1 A to amino acids 1 -251 of SEQ ID NO: 1 removed the last two B-cell epitope regions (Table 5, #8 and #9), the last two CD4+ T-cell epitope regions (Table 5, #8 and #9), and the highest scoring discontinuous B-cell epitope predicted by ElliPro (289-293). In addition, the truncation at position 251 might disrupt the seventh epitope region comprising putative B-cell and T-cell epitopes (Table 5).
[319] Rationally selected amino acid substitutions (see Table 6) were created in the truncated Shiga toxin effector polypeptide comprising amino acids 1-251 of SEQ ID NO: 1 using methods known in the art. In epitope region #0 (see Table 5), at least seven different amino acid substitutions were made and tested (see Table 6). In epitope region #0, the lysine natively located at position 1 in the mature A Subunits of Shiga-like toxin 1 (SEQ ID NO: 1) and and Shiga toxin (SEQ ID NO:2) was mutated to methionine (KIM)). In epitope region #0, the threonine natively located at position 4 in the mature A Subunits of Shiga-like toxin 1 (SEQ ID NO: 1) and and Shiga toxin (SEQ ID NO:2) was mutated to isoleucine (T4I). In epitope region #0, the serine natively located at position 8 in the mature A Subunits of Shiga-like toxin 1 (SEQ ID NO: 1) and and Shiga toxin (SEQ ID NO:2) was mutated to isoleucine (S8I). In epitope region #0, the threonine natively located at position 9 in the mature A Subunits of Shiga-like toxin 1 (SEQ ID NO: 1) and and Shiga toxin (SEQ ID NO:2) was mutated to isoleucine (T9I) and to valine (T9V). In epitope region #0, the lysine natively located at position 1 1 in the mature A Subunits of Shiga-like toxin 1 (SEQ ID NO: 1) and and Shiga toxin (SEQ ID NO:2) was mutated to alanine (Kl 1A) and to histidine (Kl 1H). The following five amino acid residues mutated in epitope region #0: Kl, T4, S8, T9, and Kl 1, were predicted by the Epitopia webserver to be solvent exposed.
[320] In epitope region #1 (see Table 5), the serine natively located at position 33 in the mature A Subunits of Shiga-like toxin 1 (SEQ ID NO: 1) and Shiga toxin (SEQ ID NO:2) was mutated to isoleucine (S33I).
[321] In epitope region #2 (see Table 5), the serine natively located at position 45 in the mature A Subunit of Shiga-like toxin 1 (SEQ ID NO: 1) was mutated to valine (S45V) and to isoleucine (S45I). In epitope region #2 (see Table 5), the aspartate natively located at position 47 in the mature A Subunit of Shiga-like toxin 1 (SEQ ID NO: 1) was mutated to glycine (D47G). In epitope region #2 (see Table 5), the asparagine natively located at position 48 in the mature A Subunit of Shiga-like toxin 1 (SEQ ID NO: 1) was mutated to valine (N48V) and to phenylalanine (N48F).
[322] In epitope region #3* (see Table 5), the aspartate natively located at position 53 in the mature A Subunit of Shiga-like toxin 1 (SEQ ID NO: 1) and Shiga toxin (SEQ ID NO:2) was mutated to alanine (D53A), glycine (D53G), and asparagine (D53N). The D53 residue was predicted by the Epitopia webserver to be solvent exposed and have an immunogenicity scale value of 5 or "high." In epitope region #3 and #3* (see Table 5), the arginine natively located at position 55 in the mature A Subunit of Shiga-like toxin 1 (SEQ ID NO: 1) and Shiga toxin (SEQ ID NO:2) was mutated to alanine (R55A), to valine (R55V), and to leucine (R55L). In epitope region #3 and #3*, the aspartate natively located at position 58 in the mature A Subunit of Shiga-like toxin 1 (SEQ ID NO: 1) and Shiga toxin (SEQ ID NO:2) was mutated to alanine (D58A), to valine (D58V), and to phenylalanine (D58F). In epitope region #3 and #3*, the proline natively located at position 59 in the mature A Subunit of Shiga-like toxin 1 (SEQ ID NO: 1) and Shiga toxin (SEQ ID NO:2) was mutated to alanine (P59A). In epitope region #3 and #3*, the glutamate natively located at position 60 in the mature A Subunit of Shiga-like toxin 1 (SEQ ID NO: 1) and Shiga toxin (SEQ ID NO:2) was mutated to isoleucine (E60I), to threonine (E60T), and to arginine (E60R). In epitope region #3 and #3*, the glutamate natively located at position 61 in the mature A Subunit of Shiga-like toxin 1 (SEQ ID NO: 1) and Shiga toxin (SEQ ID NO:2) was mutated to alanine (E61A), to valine (E61V), and to leucine (E61L). In epitope region #3 and #3*, the glycine natively located at position 62 in the mature A Subunit of Shiga-like toxin 1 (SEQ ID NO: 1) and Shiga toxin (SEQ ID NO:2) was mutated to alanine (G62A).
[323] In epitope region #4* (see Table 5), the aspartate natively located at position 94 in the mature A Subunit of Shiga-like toxin 1 (SEQ ID NO: 1) and Shiga toxin (SEQ ID NO:2) was mutated to alanine (D94A). This D94 residue was predicted by the Epitopia webserver to be solvent exposed and have an immunogenicity scale value of 5 or "high." In epitope region #4 and #4* (see Table 5), the serine natively located at position 96 in the mature A Subunit of Shiga-like toxin 1 (SEQ ID NO: l) and Shiga toxin (SEQ ID NO:2) was mutated to isoleucine (S96I). In epitope region #4 and #4* (see Table 5), the serine natively located at position 109 in the mature A Subunit of Shiga-like toxin 1 (SEQ ID NO: 1) and Shiga toxin (SEQ ID NO:2) was mutated to valine (S109V). In epitope region #4 and #4* (see Table 5), the glycine natively located at position 110 in the mature A Subunit of Shiga-like toxin 1 (SEQ ID NO: l) and Shiga toxin (SEQ ID NO:2) was mutated to alanine (Gl 10A). In epitope region #4 and #4* (see Table 5), the serine natively located at position 1 12 in the mature A Subunit of Shiga-like toxin 1 (SEQ ID NO: 1) and Shiga toxin (SEQ ID NO:2) was mutated to valine (S I 12V).
[324] In epitope region #5 (see Table 5), the glycine natively located at position 147 in the mature A Subunit of Shiga-like toxin 1 (SEQ ID NO: 1) and Shiga toxin (SEQ ID NO:2) was mutated to alanine (G147A).
[325] In epitope region 6* (see Table 5), the arginine natively located at position 179 in the mature A Subunit of Shiga-like toxin 1 (SEQ ID NO: l) and Shiga toxin (SEQ ID NO:2) was mutated to alanine (R179A). This R179 residue was predicted by the Epitopia webserver to be exposed and have an
immunogenicity value of 5 or "high." In epitope region #6 and #6* (see Table 5), the threonine natively located at position 180 in the mature A Subunit of
Shiga-like toxin 1 (SEQ ID NO: l) and Shiga toxin (SEQ ID NO:2) was mutated to glycine (T180G). In epitope region #6 and #6* (see Table 5), the threonine natively located at position 181 in the mature A Subunit of Shiga-like toxin 1 (SEQ ID NO: l) and Shiga toxin (SEQ ID NO:2) was mutated to isoleucine (T181I). In epitope region #6 and #6* (see Table 5), the aspartate natively located at position 183 in the mature A Subunit of Shiga-like toxin 1 (SEQ ID NO: 1) and Shiga toxin (SEQ ID NO:2) was mutated to alanine (D183A) and to glycine (D183G). In epitope region #6 and #6*, the aspartate natively located at position 184 in the mature A Subunit of Shiga-like toxin 1 (SEQ ID NO: 1) and Shiga toxin (SEQ ID NO:2) was mutated to alanine (D184A) or phenylalanine (D184F). In epitope region #6 and #6* (see Table 5), the leucine natively located at position 185 in the mature A Subunit of Shiga-like toxin 1 (SEQ ID NO: 1) and Shiga toxin (SEQ ID NO:2) was mutated to valine (LI 85V). In epitope region #6 and #6*, the serine natively located at position 186 in the mature A Subunit of Shiga-like toxin 1 (SEQ ID NO: 1) and Shiga toxin (SEQ ID NO:2) was mutated to alanine (S 186A) and to phenylalanine (S 186F). In epitope region #6 and #6*, the glycine natively located at position 187 in the mature A Subunit of Shiga-like toxin 1 (SEQ ID NO: 1) and Shiga toxin (SEQ ID NO:2) was mutated to alanine (G187A). In epitope region #6 and #6*, the arginine natively located at position 188 in the mature A Subunit of Shiga-like toxin 1 (SEQ ID NO: 1) and Shiga toxin (SEQ ID NO:2) was mutated to alanine (R188A) and to leucine (R188L). In epitope region #6 and #6*, the serine natively located at position 189 in the mature A Subunit of Shiga-like toxin 1 (SEQ ID NO: 1) and Shiga toxin (SEQ ID NO:2) was mutated to alanine (S189A).
[326] In epitope region #7 (see Table 5), the arginine natively located at position 248 in the mature A Subunit of Shiga-like toxin 1 (SEQ ID NO: 1) and Shiga toxin (SEQ ID NO:2) was mutated to alanine (R248A). In epitope region #7, the arginine natively located at position 251 in the mature A Subunit of
Shiga-like toxin 1 (SEQ ID NO: l) and Shiga toxin (SEQ ID NO:2) was mutated to alanine (R251A).
[327] The leucine natively located at position 49 in the mature A Subunit of Shiga-like toxin 1 (SEQ ID NO: l) and Shiga toxin (SEQ ID NO:2) was mutated to alanine (L49A). This L49 residue was predicted by the Epitopia webserver to be solvent exposed and have an immunogenicity value of 4. The arginine natively located at position 205 in the mature A Subunit of Shiga-like toxin 1 (SEQ ID NO: 1) and Shiga toxin (SEQ ID NO:2) was mutated to alanine (R205A). This R205 residue was predicted by the Epitopia webserver to be solvent exposed and have an immunogenicity value of 5 or "high."
Table 6. Amino Acid Substitutions in Exemplary Shiga Toxin Effector
Polypeptides
Figure imgf000124_0001
4* D94A 94-115 77-103
4&4* S96I 96-115 77-103
4&4* SI 09V 96-115
4&4* G110A 96-115
4&4* SI 12V 96-115
5 G147A 141-153 128-168
6* R179A 179-190 160-183
6&6* T180G 180-190 160-183
6&6* T181I 180-190 160-183
6&6* D183A 180-190 160-183
6&6* D183G 180-190 160-183
6&6* D184A 180-190
6&6* D184F 180-190
6&6* L185V 180-190
6&6* S186A 180-190
6&6* S186F 180-190
6&6* G187A 180-190
6&6* R188A 180-190
6&6* R188L 180-190
6&6* S189A 180-190
immunogenic
- R205A
residue
7 R248A 243-257 236-258
7 R251A 243-257 236-258
[328] The amino acid substitution comprising Shiga toxin effector polypeptides were tested as components of putative cytotoxic proteins with cell-targeting binding regions. The cytotoxic proteins comprised an immunoglobulin-type binding region and Shiga toxin effector region linked together to form a fusion protein. These putative cytotoxic fusion proteins were produced by expression from polynucleotides encoding them using a bacterial system known in the art.
Example 3. Empirically Testing De-Immunized Shiga Toxin Effector Polypeptides for Retention of One or More Shiga Toxin Effector Functions
[329] Various de-immunized Shiga toxin effector region polypeptides were empirically tested for retention of enzymatic activity and cytotoxicity.
[330] The retention of enzymatic activity of Shiga toxin effector polypeptides after de-immunization was tested using a ribosome inhibition assay in the context of the Shiga toxin effector polypeptide as a component of a cytotoxic protein. In certain experiments, the full-length coding sequence of the cytotoxic protein of this example began or ended with a polynucleotide encoding a Strep- tag® II to facilitate detection and purification.
[331] The ribosome inactivation capabilities of de-immunized cytotoxic proteins were determined using a cell-free, in vitro protein translation assay using the TNT® Quick Coupled Transcription/Translation kit (LI 170 Promega Madison, WI, U.S.). The kit includes Luciferase T7 Control DNA (L4821 Promega Madison, WI, U.S.) and TNT® Quick Master Mix. The ribosome activity reaction was prepared according to manufacturer's instructions. A series of 10-fold dilutions of the protein comprising a mutated Shiga toxin effector polypeptide region to be tested was prepared in an appropriate buffer and a series of identical TNT reaction mixture components were created for each dilution. Each sample in the dilution series was combined with each of the TNT reaction mixtures along with the Luciferase T7 Control DNA. The test samples were incubated for 1.5 hours at 30 degrees Celsius (°C). After the incubation, Luciferase Assay Reagent (E1483 Promega, Madison, WI, U.S.) was added to all test samples and the amount of luciferase protein translation was measured by luminescence according to manufacturer's instructions. The level of translational inhibition was determined by non-linear regression analysis of log- transformed concentrations of total protein versus relative luminescence units. Using statistical software (GraphPad Prism, San Diego, CA, U.S.), the half maximal inhibitory concentration (ICso) value was calculated for each sample using the Prism software function of log(inhibitor) vs. response (three parameters) [Y = Bottom + ((Top-Bottom) / (l+10A(X-LogIC50)))] under the heading dose-response-inhibition. The ICso for each protein comprising a de- immunized Shiga toxin effector polypeptide region and a control protein comprising a wild-type Shiga toxin effector region with no internal epitope disruptions were calculated.
[332] Exemplary Shiga toxin effector polypeptide regions which exhibited ribosome inhibition are indicated in Table 7. As reported in Table 7, a substitution-comprising construct exhibiting an ICso within 10-fold of a wild- type SLT-1A control construct is considered to exhibit ribosome inhibition activity comparable to wild-type; a construct exhibiting an ICso between 10-fold to 100-fold of a wild-type SLT-1A control is considered to exhibit attenuated activity as compared to wild-type; and a construct exhibiting an IC50 greater than
100-fold of a wild-type SLT-1 A control is considered severely impaired or inactive (severely impaired / inactive).
Table 7. Ribosome Inhibition Activities of Exemplary Shiga Toxin
Effector Polypeptides
Figure imgf000127_0001
[333] The retention of cytotoxic activity of various exemplary Shiga toxin effector polypeptides after de-immunization was tested using a target-cell -kill assay in the context of the Shiga toxin effector polypeptide as a component of a cytotoxic protein with a binding region capable of specific and high-affinity binding to an extracellular target biomolecule expressed and physically-coupled to the cellular surface of target cells (i.e. "target-expressing cells" or "target biomolecule positive cells"). The cytotoxicity levels of de-immunized cytotoxic proteins were determined using target-expressing cells as compared to cells that do not express a target biomolecule of the cytotoxic protein's binding region.
[334] Target-expressing cells were plated (2 x 103 cells per well for adherent cells, plated the day prior to protein addition or 7.5 x 103 cells per well for suspension cells, plated the same day as protein addition) in 20 μΐ, cell culture medium in 384 well plates. A series of 10-fold dilutions of each protein comprising a mutated Shiga toxin effector polypeptide region to be tested was prepared in an appropriate buffer, and 5 μΐ, of the dilutions or buffer control were added to the cells. Control wells containing only media were used for baseline correction. The cell samples were incubated with the proteins or just buffer for 3 days at 37°C and in an atmosphere of 5% carbon dioxide (CO2). The total cell survival or percent viability was determined using a luminescent readout using the CellTiter-Glo® Luminescent Cell Viability Assay (G7573 Promega Madison, WI, U.S.) according to the manufacturer's instructions.
[335] The Percent Viability of experimental wells was calculated using the following equation: (Test RLU - Average Media RLU) / (Average Cells RLU - Average Media RLU) * 100. Log polypeptide concentration versus Percent Viability was plotted in Prism (GraphPad Prism, San Diego, CA, U.S.) and log (inhibitor) versus response (3 parameter) analysis was used to determine the half-maximal cytotoxic concentration (CD50) value for the tested proteins. The CD50 for each protein comprising a de-immunized Shiga toxin effector polypeptide and wild-type control protein with no internal epitope disruptions were calculated.
[336] The cytotoxicity of exemplary Shiga toxin effector polypeptide regions is indicated in Table 8. As reported in Table 8, a substitution-comprising construct exhibiting a CD50 within 10-fold of a wild-type SLT-1A control construct is considered to exhibit cytotoxicity comparable to a wild-type; a construct exhibiting a CD50 between 10-fold to 100-fold of a wild-type SLT-1A control is considered to exhibit attenuated cytotoxicity as compared to wild-type; and a construct exhibiting a CD50 greater than 100-fold of a wild-type SLT-1 A control is considered severely impaired/inactive. Table 8. Cytotoxic Activities of Exemplary Shiga Toxin Effector
Polypeptides
Figure imgf000129_0001
[337] The term "successful" is used to mean one or more amino acid residue substitutions in a predicted epitope region resulted in a Shiga toxin effector region polypeptide which retained one or more Shiga toxin effector functions. Three substitutions (D183A, D 184A, and R188A) which were successful individually in the same epitope region (#6 & 6*) were combined to generate a de-immunized Shiga toxin effector polypeptide (D 183 A/D 184A/R188A) retaining Shiga toxin effector function comparable to wild-type (Tables 7 and 8), These results suggest that some successful amino acid substitutions in the same epitope region of a Shiga toxin effector polypeptide may be combined to create epitope disruptions with greater overall epitope disruption while still retaining significant levels of one or more Shiga toxin effector function. Similarly, both epitope regions #0 and #4 & 4* successfully tolerated multiple amino acid substitutions within their respective regions (Tables 7 and 8: K1M/K1 1A and D94A/S96I). Reinforcing the idea that various exemplary substitutions in the same epitope region may be combined to create epitope disruptions with greater overall epitope disruption while still retaining significant levels of one or more Shiga toxin effector function.
[338] In addition, other Shiga toxin effector region polypeptides were tested for Shiga toxin effector functions and epitope disruption using the methods as described in the Examples herein, where the Shiga toxin effector region polypeptides comprised multiple amino acids substitutions within a single predicted B-cell epitope region. The regions tested were the following natively positioned regions present in the mature A Subunit of Shiga-like toxin 1 (SEQ ID NO: l) and Shiga toxin (SEQ ID NO:2): 4-12, 43-52, 53-61, 104-1 12, and 180-188. These single-region, multi-substitution constructs were created in various combinations in the context of a cytotoxic protein comprising a Shiga toxin effector region comprising residues 1-251 of SLT-IA (SEQ ID NO: l). These constructs retained ribosome inhibition comparable to a wild-type SLT- IA effector construct and were selectively cytotoxic to target cells. These constructs comprised one or more of the following amino acid substitutions in various combinations with other amino acid substitutions in a single region: region 4-12: T4I, T9V, and K11H; region 43-52: S45V, D47G, N48V, N48F, and L49A; region 53-61 : D53G, D53N, R55V, R55L, D58V, E60T, E61V and E61L; region 104-112: S109V, Gl 10A, and SI 12V; region 180-188: T180G, T181I, D183G, L185V, S186F, and R188L. In addition, Western analysis of these constructs showed reduced or abolished recognition of each construct by one or more antibodies that can recognize wild-type SLT-IA (mAbl, pAbl, and pAb2 described in Example 4).
[339] In addition, epitope region #7 is disrupted by the substitution R248A or R251 without any significant effect on either ribosome inhibition activity or cytotoxicity. R248A or R251A may be successfully introduced into the exemplary Shiga toxin effector region polypeptides described above without altering either ribosome inhibition or cytotoxicity.
[340] Individual epitope disruptions mentioned above as well as new disruptions were combined to create various combinations of Shiga toxin effector polypeptides (Table 9) comprising disruptions of two or more epitope regions, and then empirically examined for retention of Shiga toxin effector functions as described in this Example. Table 9 lists the activities exhibited by constructs with combinations of amino acid substitutions, within a single epitope region or in as many as five different epitope regions, using the terms described previously.
Table 9. Multi-Epitope-Region Amino-Acid-Substitution Combinations in De-Immunized Shiga Toxin Effector Polypeptides and Cytotoxic Proteins
Figure imgf000131_0001
Figure imgf000132_0001
[341] These results suggest generally that most if not all successful amino acid substitutions in one epitope region of a Shiga toxin effector polypeptide, meaning any substitution empirically shown to retain a Shiga toxin effector function and predicted to disrupt an epitope, may be combined with most if not all other successful amino acid substitutions in a different epitope region to form a de-immunized Shiga toxin effector polypeptide with multiple epitope regions disrupted while still retaining at least one Shiga toxin effector function. Example 4. Empirically Testing De-Immunized Shiga Toxin Effector
Polypeptides for Disruption of Antigenic and/or Immunogenic Epitope(s)
[342] Experimental testing was performed to confirm disruption of B-cell epitopes based on empirically verifiable epitopes recognized by known antibodies. Western analyses were performed to determine epitope disruptions under denaturing conditions. Enzyme-linked immunosorbent assay (ELISA) analyses were performed to determine epitope disruptions under more native protein folding conditions (i.e. non-denaturing conditions).
[343] Cytotoxic proteins comprising Streptag® II and wildtype Shiga toxin effector polypeptide regions or de-immunized Shiga toxin effector polypeptide regions were loaded in equal amounts to replicate 4-20% sodium dodecyl sulfate (SDS) polyacrylamide gels (Lonza, Basel, CH) and electrophoresed under denaturing conditions. The resulting gels were either analyzed by Coomassie staining or transferred to polyvinyl difluoride (PVDF) membranes using the iBlot® (Life Technologies, Carlsbad, CA, U.S.) system according to manufacturer's instructions. The resulting membranes were probed under standard conditions using the following antibodies: rabbit polyclonal a- NWSHPQFEK (A00626, Genscript, Piscataway, NJ, U.S.) which recognizes the polypeptide NWSHPQFEK also known as Streptag® II, mouse monoclonal a- StxA (anti-SLT-ΙΑ mAbl or mAbl) (BEI R-867 BEI Resources, Manassas, VA, U.S.), rabbit polyclonal antibody a-SLT-lA (anti-SLT-ΙΑ pAbl or pAbl) (Harlan Laboratories, Inc. Indianapolis, IN, U.S., custom antibody production, raised against SLT-1A amino acids 1-251), and rabbit polyclonal antibody a- SLT-1A (anti-SLT-ΙΑ pAb2 or pAb2) (Genscript, Piscataway, NJ, U.S., custom antibody production), which was raised against the peptides RGIDPEEGRFN and HGQDSVRVGR. The peptide sequence RGIDPEEGRFNN spans the putative B-cell epitope region #3 (Table 5), and the peptide sequence
HGQDSVRVGR is located at 214-223 in SLT-1A and StxA. Membrane bound antibodies were detected using standard conditions and, when appropriate, using horseradish peroxidase (HRP) conjugated secondary antibodies (goat anti-rabbit- HRP or goat anti-mouse-HRP, Thermo Scientific, Rockford, IL, U.S.). Figures 2-5 show Western blots with the lanes of the gels and/or membranes numbered and the figure legends indicate by the same respective numbering which Shiga toxin effector regions were comprised within the protein loaded into each lane.
[344] The D58A substitution successfully disrupted one of the epitopes recognized by the polyclonal a-SLT-lA pAb2 (Figure 2). Similarly, the D58A/G110A/G147A triple substitution and S33I/S45I/D58A/G1 10A/G147A quintuple substitution mutants showed strong disruption of at least one of the epitopes recognized by a-SLT-lA pAb2 (Figure 3; Figure 4) and partial disruption of at least one of the epitopes recognized by a-SLT-lA pAbl (Figure 3).
[345] The S45I/G1 10A/G147A and S33I/G110A/G147A triple substitution mutants showed partial disruption of at least one of the epitopes recognized by a-SLT-lA pAbl (Figure 3). The S45I/G1 10A/G147A triple mutant strongly disrupted the epitope recognized by the monoclonal antibody mAbl and partially disrupted the epitope recognized by the polyclonal a-SLT-lA pAb2 (Figure 3; Figure 4). The D58A/G1 10A/G147A triple mutant very effectively disrupted the epitope recognized by the monoclonal antibody mAb 1 and at least one of the epitopes recognized by the polyclonal a-SLT-lA pAb2 (Figure 3; Figure 4).
[346] The D 183 A/D 184A/R188A triple mutant showed very effective disruption of the epitope recognized by the monoclonal antibody mAb 1 (Figure 5). The D58A/G1 10/G147A/R188A quadruple mutant very effectively disrupted the epitope recognized by the monoclonal antibody mAbl and at least one of the epitopes recognized by the polyclonal a-SLT-lA pAb2 and partially disrupted at least one of the epitopes recognized by a-SLT-lA pAbl (Figure 5).
[347] It is likely that the epitopes disrupted in the D58A/G110A/G147A triple, S45I/G1 10A/G147A triple, and D58A/G110A/G147A/R188A quadruple mutants (one recognized by mAbl and others recognized by pAb2) most likely reside in two non-continuous regions. Thus, the D58A/G1 10A/G147A triple, S45I/G1 10A/G147A triple, and D58A/G110A/G147A/R188A quadruple substitution mutants each comprised a de-immunized Shiga toxin effector region polypeptide verified empirically to have at least two different epitopes disrupted simultaneously.
[348] Similarly, it is likely that certain dominant epitopes disrupted in the D58A/G110A/G 147 A triple, S45I/G1 10A/G147A triple, S33I/G110A/G147A triple, D58A/G1 10A/G147A/R188A quadruple, and
S33I/S45I/D58A/G1 10A/G147A quintuple mutants (epitopes recognized by pAbl and pAb2) most likely reside in at least two non-continuous regions. Thus, D58A/G110A/G147A triple, S45I/G1 10A/G147A triple,
S33I/G1 10A/G147A triple, D58A/G110A/G147A/R188A quadruple, and S33I/S45I/D58A/G1 10A/G147A quintuple mutants probably comprised a de- immunized Shiga toxin effector region polypeptide verified empirically to have at least two different epitopes disrupted simultaneously.
[349] A standard ELISA was used to measure the ability of mAbl to recognize a de-immunized Shiga toxin effector region with multiple epitope regions disrupted in the context of a cytotoxic protein. The cytotoxic protein bound the target biomolecule of its scFv binding region. The wells of Nunc MaxiSorp® plates in phosphate buffered saline (IX PBS) (Hyclone Brand, Fisher Scientific, Waltham, MA, U.S.) were coated with recombinant human target protein of the binding region of the cytotoxic protein. The plates were incubated overnight at 4°C. The wells were washed with IX PBS 0.05% Tween-20 (PBS-T), and nonspecific binding was blocked by incubating the wells with 3% milk in PBS-T for one hour at room temperature. A cytotoxic protein comprising a Streptag® II and a de-immunized Shiga toxin effector region (D58A/G1 10A/G147A/R188A) was added to the wells at a concentration determined to be above the binding dissociation constant (KD). AS a positive control and reference for wild-type activity, a cytotoxic protein comprising a wild-type Shiga toxin effector region and a Streptag® II was added to the wells at the same concentrations.
[350] The plates were incubated at room temperature for one hour to allow for cytotoxic protein binding under non-denaturing conditions. The wells were washed with PBS-T and then incubated with either PBS-T or the mouse monoclonal antibody anti-SLT-lA mAbl for one hour at room temperature. The wells were washed in PBS-T and then incubated with the detection antibodies: HRP-conjugated antibody directed to Streptag® II or an anti-mouse-HRP- conjugated antibody. The wells were washed in PBS-T and then incubated with Pierce TMB Ultra (Thermo Scientific Inc., Rockford, IL, U.S.). The reactions were stopped with 250 mM hydrochloric acid (HC1). Products of HRP activity were detected by a plate reading device measuring absorbance (Abs) of light set to the wavelength of 450 nanometers (nm). The measured absorbance values were corrected for background by subtracting the absorbance values for coated, blocked wells incubated with PBS instead of any Shiga toxin construct.
[351] Both cytotoxic proteins bound to the human, recombinant protein, target biomolecule of the scFv as measured by high absorbance values for the Streptag® II antibody (Figure 6). The cytotoxic protein comprising the de- immunized Shiga toxin effector region (D58A/G110A/G147A/R188A) was not recognized by the monoclonal antibody anti-SLT-1 A mAbl (Figure 6). The positive control cytotoxic protein, which comprised the wild-type Shiga toxin effector polypeptide, was bound by the antibody anti-SLT-lA mAbl (Figure 6). These results indicated that the epitope recognized by anti-SLT-lA mAbl was present in the natively folded, wild-type Shiga toxin effector region, but that epitope was disrupted by the combination of mutations
D58A/G110A/G147A/R188A in the natively folded, de-immunized Shiga toxin effector region.
Example 5. Predicting the Disruption of Antigenic and/or Immunogenic Epitopes in Shiga Toxin Effector Polypeptides
[352] Each substitution made in Example 4 with an aim to de-immunize a Shiga toxin effector polypeptide while retaining Shiga toxin effector functions was checked for abolishment of the predicted B-cell epitope in the epitope region comprising the substitution using the BcePred webserver with the following: flexibility readout with the default settings of hydrophilicity 2, accessibility 2, exposed surface 2.4, antigenic propensity 1.8, flexibility 1.9, turns 1.9, polarity 2.3, and combined 1.9 (Saha S, Raghava G, Lecture Notes in Comput Sci 3239: 197-204 (2004)). Table 10 shows the substitution present in the analysis and the result of the B-cell epitope prediction in the last column. Of note, epitope regions #0 (1-15) and #7 (243-257) were not predicted in wild-type SLT-1A by the BcePred flexibility approach with the default settings. The substitutions tested (see Table 6) did not create de novo any predicted B-cell epitopes by the BcePred flexibility approach (see e.g. Table 10), including KIM, S8I, T9I, Kl 1A in epitope region #0; D94A in epitope region #4*; and S96I in epitope regions #4 and 4*. Additionally, the results for other substitutions analyzed using the BcePred computational approach are listed in Table 10 that were not yet empirically tested.
Table 10. B-Cell Epitope Predictions after Amino Acid Substitution
Figure imgf000136_0001
& 3* 55-66 D58A eliminated & 3* 55-66 D58F eliminated & 3* 55-66 P59A eliminated & 3* 55-66 P59F eliminated & 3* 55-66 E60I eliminated & 3* 55-66 E60T eliminated & 3* 55-66 E60R no change & 3* 55-66 E61A eliminated & 3* 55-66 E61V eliminated & 3* 55-66 E61L eliminated & 3* 55-66 G62A eliminated
4* 94-115 D94A no change & 4* 96-115 S96I no change & 4* 96-115 SI 09 V eliminated & 4* 96-115 G1 10A eliminated & 4* 96-115 SI 12V eliminated
5 141-153 G147A eliminated
6* 179-190 R179A no change & 6* 180-190 T180G no change & 6* 180-190 T181I no change & 6* 180-190 D183A no change & 6* 180-190 D183G no change & 6* 180-190 D184A eliminated & 6* 180-190 D184F eliminated & 6* 180-190 L185V eliminated & 6* 180-190 S186A eliminated & 6* 180-190 S186F eliminated & 6* 180-190 G187A eliminated & 6* 180-190 R188A eliminated & 6* 180-190 R188L eliminated & 6* 180-190 S189A eliminated
7 243-257 S247I eliminated
7 243-257 R248A eliminated
7 243-257 R251A eliminated
8 254-268 D264A eliminated
8 254-268 G265A eliminated
8 262-278 (SLT-2A) G264A eliminated
9 285-293 T286A eliminated
9 285-293 T286I eliminated [353] The Western analysis of SLT-1A wildtype compared to SLT-1A D58A (Figure 2) showed that the BcePred computational flexibility approach accurately predicted the presence of a B-cell epitope at position 55-66 of SLT- 1A (Table 1), and the disruption of that epitope region by the D58A substitution was also accurately predicted (Table 10).
Example 6. Empirically Testing the Relative Immunogenicity of a De- Immunized Shiga Toxin Effector Polypeptide Compared to a Wild-Type Shiga Toxin Effector Polypeptide Using a Mammalian Model
[354] In this example, the relative immunogenicity of a de-immunized cytotoxic protein of the invention compared to a non-de-immunized cytotoxic protein was determined using a mammalian model of the human immune system. A murine model of mammalian immune systems was used to compare the relative immunogenicity of an exemplary cytotoxic protein comprising an exemplary de-immunized Shiga toxin effector polypeptide to the parental cytotoxic protein comprising a Shiga toxin effector region with only wild-type sequences. Because bacterium-derived Shiga toxin effector region polypeptides are foreign (or non-self) molecular structures to mammals, it was expected that the wild-type Shiga toxin effector polypeptide would exhibit some level of immunogenicity. The relative immunogenicity of a non-mammalian protein determined using mice are generally indicative of its relative immunogenicity for all mammals.
[355] An in-solution ELISA assay was used to determine the relative amount of serum murine antibodies that were specific to different cytotoxic protein samples: cytotoxic proteins comprising either a wild-type Shiga toxin effector polypeptide (amino acids 1-251 of SLT-1A) or an exemplary de-immunized Shiga toxin effector region polypeptide (amino acids 1-251 of SLT-1A with certain amino acid substitutions). Female BALB/c mice were randomly assigned to groups to form groups with six mice each. First, serum samples were collected from each mouse prior to exposure to a cytotoxic protein. Next, each mouse in a group was administered 0.25 mg/kg per dose of the cytotoxic protein comprising either a wild-type (amino acids 1-251 of SLT-1A) or an exemplary de-immunized Shiga toxin effector region (amino acids 1-251 of SLT-1A comprising D58A/G1 10A/G147A/R188A) by intra-peritoneal injection three times a week over a duration of two weeks for a total of six injections over twelve days. During and after the course of cytotoxic protein administration, murine sera were collected from mice from all the groups to observe anti- "administered protein" levels using an in-solution ELISA assay.
[356] The in-solution anti-"cytotoxic protein" ELISA assay was performed as follows. The same cytotoxic protein used for injections in a mouse group was incubated overnight at 4°C in solution with the serum of mice from that group, and then the immune complex (consisting of the cytotoxic protein bound to any induced antibodies in the serum) was captured using ELISA plate wells coated with the appropriate target protein. Captured immune complexes comprising murine IgGs were detected using a horseradish-peroxidase-conjugated, anti- mouse IgG, secondary antibody. ELISA plates were developed to detect horsereadish peroxidase activity, and the horsereadish peroxidase activity or "ELISA signal" was measured at 450 nm using a plate reader. The "ELISA signal" or "ELISA values" were calculated as the absorbance values after subtracting the background signal as measured with a "no serum" negative control. For this in-solution ELISA assay and setup, greater ELISA values indicate stronger immune responses (antibody induction).
[357] None of the mice in any group were measured by this in-solution ELISA assay to have pre-formed serum antibodies recognizing either cytotoxic protein prior to exposure to a cytotoxic protein via injection. Thus, any post- administration detection of anti-"cytotoxic protein" antibodies in these mice using the in-solution ELISA assay represents induced de novo antibody formation which occurred after administration.
[358] For the relative immunogenicity study of this Example, the same cytotoxic protein injected into a group of mice was used in the ELISA assay to capture serum antibodies from the mice of that group. In other words, the antibodies present in the sera from mice in the "wild-type Shiga toxin effector region" group were captured in the ELISA assay with the cytotoxic protein comprising a wild-type Shiga toxin effector region, and the antibodies present in sera from the mice in the "de-immunized Shiga toxin effector region polypeptide" group were captured in the ELISA assay with the exemplary cytotoxic protein comprising the exemplary de-immunized Shiga toxin effector region polypeptide (D58A/G1 10A/G147A/R188A). [359] At Day 15 (3 days after the administration of the sixth dose) and Day 22 (10 days after the administration of the sixth dose), an anti-"cytotoxic protein" IgG response was measured by the in-solution ELISA assay described above (Figure 7). In Figure 7, the symbols represent individual mice: the filled symbols represent mice administered a cytotoxic protein comprising wild-type Shiga toxin effector region and the open symbols represent mice administered an exemplary cytotoxic protein comprising a de-immunized Shiga toxin effector region polypeptide. In Figure 7, the vertical lines indicate the mean IgG response signal for each group respectively.
[360] Mice in the group administered the cytotoxic protein comprising a wild- type Shiga toxin effector region had a higher magnitude of antibody response as shown by the ELISA signal than the mice in the group administered the cytotoxic protein comprising the de-immunized Shiga toxin effector region (D58A/G1 10A/G147A/R188A) at both Day 15 and 22 (Figure 7). The mean ELISA signal (quantitating antibody response) for the "de-immunized Shiga toxin effector region polypeptide" group was 25% (Day 15) and 39% (Day 22) of the "wild-type Shiga toxin effector region" group. The ELISA signal differences between the "de-immunized Shiga toxin effector region polypeptide" and the "wild-type Shiga toxin effector region" groups were statistically significant based on t-tests (p value was less than 0.005). Using a nominal absorbance value cutoff of 0.9 Abs units to represent a "strong" antibody response, 6/6 (100%) mice in the "wild-type Shiga toxin effector region" group had a strong antibody response at Days 15 or 22, whereas only 3/6 (50%) mice in the "de-immunized Shiga toxin effector region polypeptide" group had a strong antibody response.
[361] The exemplary cytotoxic protein comprising the de- immunized Shiga toxin effector region polypeptide (D58A/G1 10A/G147A/R188A) showed reduced immunogenicity in a mammalian model (Figure 7). The decrease in the overall magnitude of antibody induction in mice in the "de-immunized Shiga toxin effector region polypeptide" group, as well as the reduction in the number of mice in this group which induced a potent antibody response, as compared to the "wild-type Shiga toxin effector region" group shows that the de-immunized Shiga toxin effector region polypeptide (D58A/G1 10A/G147A/R188A) was successfully de- immunized (i.e. has reduced immunogenic potential in mammals), and the exemplary cytotoxic protein comprising it is a de-immunized cytotoxic protein (i.e. has reduced immunogenic potential in mammals).
[362] This exemplary de-immunized cytotoxic protein comprised a Shiga toxin effector region polypeptide comprising four different B-cell epitope region disruptions while retaining three or more Shiga toxin effector functions:
catalytic ribosome inhibition, intracellular routing, and cytotoxicity (Table 9). Additionally, the de-immunized Shiga toxin effector region polypeptide of this cytotoxic protein was shown to have disrupted epitopes recognized by mAbl, pAb2, and pAbl by western blot (Figure 5) and mAbl by an ELISA assay (Figure 6). Therefore, this exemplary cytotoxic protein is a de-immunized cytotoxic protein comprising a de-immunized Shiga toxin effector region polypeptide which has both reduced antigenicity and immunogenicity to mammalian immune systems. The antigenicity and/or immunogenicity of this exemplary cytotoxic protein may be further reduced by introducing additional mutations in the same or additional predicted B-cell epitope regions.
Additionally, alternative substitutions at the same or different positions in the already disrupted B-cell epitope regions will result reduced relative
immunogenicity.
[363] The relative immunogenicities of various exemplary de-immunized Shiga toxin effector region polypeptides or exemplary cytotoxic protein comprising various de-immunized Shiga toxin effector polypeptide regions are tested in a similar manner. Certain exemplary de-immunized Shiga toxin effector region polypeptides, including 1. (1-251 : KIM/ Kl 1A/ S33I/ S45V D58A/ Gl 10A/ G147A/ R188A), 2. (1-251 : KIM/ Kl 1A/ S33I/ S45V D58A/ G110A/ G147A/ D183A/ D184A/ R188A), 3. (1-251 : KIM/ Kl 1A/ S33I S45I/ D58A/ E60V G1 10A/ G147A/ D183A/ D 184/ R188A), 4. (1-251 : K1M/ K1 1A/ S33I/ S45I/ R55A/ D58A/ P59A/ E60I/ E61A/ G62A/ Gl 10A/ G147A/ D183A/ D184A/ R188A), 5. (1-251 : KIM/ Kl 1A/ S33I/ S45I/ D58A/ Gl 10A/ G147A/ D183A/ D184A/ S189A), and 6. (1-251 : KIM/ Kl 1A/ S33I/ S45I/ R55A/ D58A/ P59A/ E60I/ E61A/ G62A/ Gl lOA/ G147A/ D183A/ D184/ R188A/ R205A), and SEQ ID NOs:4-52 are compared to Shiga toxin effector polypeptides comprising only wild-type amino acid sequences and/or parental cytotoxic proteins comprising wildtype Shiga toxin effector polypeptide regions using animal models and assays described herein or known to the skilled worker. [364] In this example, mice are intravenously administered either the de- immunized or wildtype forms 4 times at 7 day intervals. Blood samples are taken from the injected mice and tested by ELISA assays for reactivity to the cytotoxic proteins and/or the Shiga toxin effector polypeptide. Relatively reduced immunogenic responses will be measured in mice injected with certain exemplary de-immunized Shiga toxin effector polypeptides or cytotoxic protein comprising the same as compared to molecules comprising Shiga toxin effector region polypeptides comprising only wild-type amino acid sequences.
[365] Certain exemplary de-immunized cytotoxic protein comprising exemplary de-immunized Shiga toxin effector region polypeptides comprising multiple B-cell epitope region disruptions will retain at a significant level of one or more Shiga toxin effector function: catalytic ribosome inhibition, intracellular routing, and cytotoxicity and have reduced recognition by pre-formed antibodies recognizing anti-Shiga-like Toxin A Subunit antibodies both western blot and/or an ELISA assay. These exemplary cytotoxic protein comprising de-immunized Shiga toxin effector region polypeptides with multiple B-cell epitope region disruptions are de-immunized Shiga toxin effector region polypeptides with reduced antigenicity and/or immunogenicity. Summary
[366] The previous examples demonstrated that B-cell epitope regions within Shiga toxin effector region polypeptides can be disrupted by amino acid substitutions and result in reductions in both antigenicity and immunogenicity. The amino acid residue substitutions within predicted epitope regions of Shiga toxin effector region polypeptides in the context of a cytotoxic protein which retained at least one Shiga toxin function are summarized in Table 1 1. All of the exemplary substitutions resulted in Shiga toxin effector regions that functionally retained high cytotoxicity with the concomitant disruption of one or more B-cell epitopes except the substitution R179A interfered with two or more Shiga toxin effector functions. Table 11. Summary of Substitutions in B-Cell Epitope Regions Which Retain Shiga Toxin Effector Functions natively positioned amino acid positions
Epitope Ribosome
B-Cell Epitope Region Substitution(s) Prediction Inhibition Cytotoxicity
0: 1-15 K1M/K11A no change YES YES
0: 1-15 S8I no change YES YES
0: 1-15 T9I no change YES YES
1: 27-37 S33I eliminated YES YES
2: 39-48 S45I eliminated YES YES
3*: 53-66 D53A no change YES YES
3/3*: 55-66 R55A no change YES YES
3/3*: 55-66 D58A eliminated YES YES
3/3*: 55-66 D58F eliminated YES YES
3/3*: 55-66 P59A eliminated YES YES
3/3*: 55-66 E60I eliminated YES YES
3/3*: 55-66 E60R no change YES YES
3/3*: 55-66 E61A eliminated YES YES
3/3*: 55-66 G62A eliminated YES YES
4*: 94-115 D94A/S96I no change YES YES
6: 180-190 D183A no change YES YES
6: 180-190 D184A eliminated YES YES
6: 180-190 D184F eliminated YES YES
6: 180-190 R188A eliminated YES YES
D183A/ D184A/
6: 180-190 eliminated YES YES
R188A
immunogenic
R205A eliminated YES YES residue
3/3*, 4/4* E60I/ G110A eliminated YES YES
3/3*, 5 E60I/ G147A eliminated YES YES
2, 6/6* S45I/R188A eliminated YES YES
S33I/ G110A/
1, 4/4*, 5 eliminated YES YES
G147A
S45I/
2, 4/4*, 5 eliminated YES YES
G110A/G147A
D58A/ G110A/
3/3*, 4/4*, 5 eliminated YES YES
G147A
E60I/ G110A/
3/3*, 4/4*, 5 eliminated YES YES
G147A
S45I/ D58A/ E60I/
2, 3/3*, 4/4*, 5 eliminated YES YES
G110A/ G147A
S45I/ D58A/ E60I/
2, 3/3*, 4/4*, 5 eliminated YES YES
G62A/ G110A/ G147A
S45I/ G1 10A/
2, 4/4*, 5, 6/6* G147A/ D183A/ eliminated YES YES
D184A/ R188A
D58A/ G110A/
3/3*, 4/4*, 5, 6 eliminated YES YES
G147A/ S186A
D58A/ G110A/
3/3*, 4/4*, 5, 6/6* eliminated YES YES
G147A/ G187A
D58A/ G110A/
3/3*, 4/4*, 5, 6/6* eliminated YES YES
G147A/ R188A
D58A/ G110A/
3/3*, 4/4*, 5, 6/6* eliminated YES YES
G147A/ S189A
D58A/ G110A/
3/3*, 4/4*, 5, 6/6* G147A/ S 186A/ eliminated YES YES
R188A
D58A/ G110A/
3/3*, 4/4*, 5, 6/6* G147A/ G187A/ eliminated YES YES
R188A
S33I/ S45I/ D58A/
1, 2, 3/3*, 4/4*, 5 eliminated YES YES
G110A/ G147A
S45I/ D58A/ E60I/
G110A/ G147A/
2, 3/3*, 4/4*, 5, 6/6* eliminated YES YES
D183A/ D184A/
R188A
S45I/ D58A/ E60I/
G62A/ G110A/
2, 3/3*, 4/4*, 5, 6/6* eliminated YES YES
G147A/ D183A/
D184A/ R188A
[367] Despite the challenges predicting successful substitutions a priori, the data provided in the Examples herein give reasons to believe that certain amino acid substitutions are likely to successfully reduce antigenicity and/or immunogenicity while maintaining significant Shiga toxin effector function(s).
For example, substitutions at specific amino acid positions shown herein as successfully tolerating substitutions (Table 11) are most likely to be successful for retaining at least one Shiga toxin effector function when substituted with certain other amino acids. The demonstration that cytotoxic proteins comprising Shiga toxin effector regions retained cytotoxicity when multiple single amino acid substitutions (predicted to disrupt an epitope region and that retained cytotoxicity) were combined (Table 9; Table 1 1) suggests that successful single amino acid substitution may generally be combined with other successful amino acid substitutions in a different epitope region to generate de-immunized Shiga toxin effector polypeptides which retain significant Shiga toxin effector function(s). Similarly, the demonstration that cytotoxic proteins comprising Shiga toxin effector regions with multiple single amino acid substitutions within the same epitope region retained enzymatic activity (Table 9; Table 11) suggests that successful single amino acid substitution in the same epitope region may generally be combined with other single amino acid substitutions in the same epitope region to generate de-immunized Shiga toxin effector polypeptides which retain significant Shiga toxin effector function(s). The fact that cytotoxic proteins comprising Shiga toxin effector region polypeptides with multiple single amino acid substitutions within the same epitope region retained cytotoxicity (Table 9; Table 11) suggests that successful single amino acid substitution in an epitope region may be combined with other single amino acid substitutions in the same epitope region to generate de-immunized Shiga toxin effector polypeptides which retain significant Shiga toxin effector function(s).
[368] The empirical data demonstrated that certain substitutions (KIM, S8I, T9I, K11A, S33I, S45I, D53A, R55A, D58A, D58F, P59A, E60I, E60R, E61A, G62A, D94A, S96I, G110A, G147A, D183A, D 184A, D 184F, R188A, R205A, and/or combinations thereof) and certain positions tolerated substitutions (1, 4, 8, 9, 11, 33, 45, 48, 53, 55, 57, 58, 59, 60, 61, 62, 94, 96, 109, 110, 147, 180, 181, 183, 184, 185, 186, 187, 188, 189, 205, 248, and 251) while retaining a significant level of activity for at least one Shiga toxin effector function. This empirical data suggest certain other epitope disrupting substitutions and combinations of epitope disrupting substitutions which may be used to generate de-immunized Shiga toxin effector polypeptides which retain significant Shiga toxin effector function(s). It is predictable that other amino acid substitutions to amino acid residues of a conservative functional group will also be tolerated. For example, other substitutions known to the skilled worker to be similar to any of KIM, T4I, S8I, T9V, T9I, K11A, S33I, S45V, S45I, D47G, N48V, N48F, L49A, D53A, D53G, D53N, R55A, R55L, I57F, D58A, D58F, P59A, P59F, E60I, E60T, E60R, E61A, E61V, E61L, G62A, D94A, S96I, S 109V, G110A, S I 12V, G147A, T180G, T181I, D183A, D183G, D 184A, D 184F, L185V, S 186A, S186F, G187A, R188A, R188L, S 189A, R205A, R248A, or R251A will also be able to disrupt an epitope while maintaining at least one Shiga toxin effector function. In particular, amino acid substitutions to conservative amino acid residues similar to KIM, T4I, S8I, T9V, T9I, K11A, S33I, S45V, S45I, D47G, N48V, N48F, L49A, D53A, D53G, D53N, R55A, R55L, I57F, D58A, D58F, P59A, P59F, E60I, E60T, E60R, E61A, E61V, E61L, G62A, D94A, S96I, S109V, G110A, SI 12V, G147A, T180G, T181I, D183A, D183G, D184A, D184F, L185V, S186A, S186F, G187A, R188A, R188L, S189A, R205A, R248A, or R251 A will have the same effect. Examples of similar conservative amino acid substitutions include Kl to A, G, V, L, I, F, and H; T4I to A, G, V, L, F, M, and S; S8 to A, G, V, L, F, and M; T9 to A, G, L, F, M, and S; Kl 1 to G, V, L, I, F, and M; S33 to A, G, V, L, F, and M; S45 to A, G, L, F, and M; T45 to A, G, V, L, I, F, and M; D47 to A, V, L, I, F, S, and Q; N48 to A, G, L, I, and M; L49 to G; D53 to V, L, I, F, S, and Q; R55 to G, I, F, M, Q, S, K, and H; D58 to G, V, L, I, S, and Q; P59 to G; E60 to A, G, V, F, S, Q, N, D, and M; E61 to G, I, F, S, Q, N, D, M, and R; D94 to G, V, L, I, F, S, and Q; S96 to A, G, V, L, F, and M; S109 to A, G, I, L, F, and M; T109 to A, G, V, I, L, F, and M; SI 12 to A, G, L, I, F and M; T180 to A, V, L, I, F, M, and S; T181 to A, G, V, L, F, M, and S; D183 to V, L, I, F, S, and Q; D184 to G, V, L, I, S, and Q; LI 85 to A and G; S186 to G, V, I, L, F, and M; R188 to G, V, L, I, F, M, Q, S, K, and H; S189 to G, V, I, L, F, and M; R204 to A, G, V, L, I, F, M, Q, S, K, and H; R205 to A, G, V, L, I, F, M, Q, S, K, and H; S247 to A, G, V, I, L, F, and M; Y247 to A, G, V, L, I, and F, R248 to G, V, L, and I; R250 to A, G, V, L, I, and F; and R251 to G, V, L, and I.
[369] Amino acid substitutions which remove charge, polarity, and/or reduce side chain length will also be able to disrupt an epitope while maintaining at least one Shiga toxin effector function. For example, substituting A, G, V, L, I, P, C, M, F, S, D, N, Q, H, and K for amino acid residue Kl, T4, S8, T9, Kl 1, S33, S45, D47, N48, L49, D53, R55, 157, D58, Ρ59, E60, E61, G62, D94, S96, S109, T109, G110, S112, G147, T180, T181, D183, D184, L185, S186, G187, R188, SI 89, R205, R248, or R251 such that side chain charge is removed, polarity is removed, and/or side chain length is reduced. In particular, the following amino acid substitutions will be able to disrupt an epitope while maintaining at least one Shiga toxin effector function: D47, D53, D58, D94, D183, D184, D264 to A, G, V, L, I, S, and ; E60 or E61 to A, G, L, V, I, S, N, Q, D, and M; G62, Gl 10, G147, G187, or G265 to A; K 1 or Kl 1 to A, G, L, V, I, F, C, M, P, S, T, N, H, and Q; L49 or LI 85 to A and G; N48 to A, G, V, L, and I; R55, R188, R205, R247, R248, R250, or R251 to A, G, L, V, I, S, Q, K, M, F, and H; S33, S45, S96, S109, SI 12, S 186, or S 189 to A, G, V, and L, and T4, T9, T45, T109, T180, T181, T286 to A, G, V, L, I, M and F.
[370] In addition, amino acid substitution in one epitope region of a Shiga toxin effector polypeptide which disrupts an epitope while retaining significant Shiga toxin effector function is generally predicted to be combinable with other amino acid substitutions in the same or a different epitope region which disrupts an epitope while retaining significant Shiga toxin effector function to form a de- immunized Shiga toxin effector polypeptide with multiple epitope regions disrupted while still retaining a significant level of a Shiga toxin effector function. For example, KIM, S8I, T9I, S9I, K11A, S33I, S45I, D53A, R55A, D58A, D58F, P59A, E60I, E60R, E61A, G62A, D94A, S96I, G110A, G147A, D183A, D184A, D184F, S186A, G187A, R188A, S 189A, and/or R205A may be combined where possible with KIM, S8I, T9I, S9I, Kl 1A, S33I, S45I, D53A, R55A, D58A, D58F, P59A, E60I, E60R, E61A, G62A, D94A, S96I, Gl 10A, G147A, D183A, D184A, D 184F, S 186A, G187A, R188A, S189A, and/or R205A to create de-immunized Shiga toxin effector region polypeptides of the invention.
Example 7. A Cytotoxic Protein Comprising a De-Immunized Shiga Toxin Effector Polypeptide and a Binding Region Specific to CD20 (aCD20 fused with SLT-1A)
[371] In this example, the Shiga toxin effector region is a de-immunized Shiga toxin effector polypeptide derived from the A subunit of Shiga-like Toxin 1
(SLT-1A) and comprising one or more de-immunizing amino acid substitutions described in the previous examples. An immunoglobulin-type binding region aCD20-antigen is derived from an immunoglobulin-type domain recognizing human CD20 (see e.g. Haisma et al, Blood 92: 184-90 (1999); Geng S et al, Cell Mol Immunol 3: 439-43 (2006); Olafesn T et al., Protein Eng Des Sel 23: 243-9 (2010)), which comprises an immunoglobulin-type binding region capable of binding an extracellular part of CD20. CD20 is expressed on multiple cancer cell types, such as, e.g., B-cell lymphoma cells, hairy cell leukemia cells, B-cell chronic lymphocytic leukemia cells, and melanoma cells. In addition, CD20 is an attractive target for therapeutics to treat certain autoimmune diseases, disorders, and conditions involving overactive B-cells.
Construction, Production, and Purification of the Cvtotoxic Protein SLT- lA::aCD20
[372] The immunoglobulin-type binding region aCD20 and Shiga toxin effector region (such as, e.g., SEQ ID NOs:4-52) are linked together. For example, a fusion protein is produced by expressing a polynucleotide encoding the aCD20-antigen-binding protein SLT-lA::aCD20 {see, e.g., SEQ ID NOs: 53, 54, 55, and 56). Expression of the SLT-lA::aCD20 cytotoxic protein is accomplished using either bacterial and/or cell-free, protein translation systems as described in the previous examples or known to the skilled worker.
Determining the In Vitro Characteristics of the Cvtotoxic Protein SLT- lA::aCD20
[373] The binding characteristics, the maximum specific binding (Bmax) and equilibrium binding constants (KD), of the cytotoxic protein of this example for CD20+ cells and CD20- cells is determined by a fluorescence-based, flow- cytometry assay. The Bmax for SLT-lA::aCD20 to CD20+ cells is measured to be approximately 50,000-200,000 MFI with a KD within the range of 0.01-100 nM, whereas there is no significant binding to CD20- cells in this assay.
[374] The ribosome inactivation abilities of the SLT-lA::aCD20 cytotoxic protein is determined in a cell-free, in vitro protein translation as described above in the previous examples. The inhibitory effect of the cytotoxic protein of this example on cell-free protein synthesis is significant. The ICso of SLT- lA::aCD20 on protein synthesis in this cell-free assay is approximately 0.1-100 pM.
Determining the Cvtotoxicitv of the Cvtotoxic Protein SLT-lA::aCD20 Using a CD20+ Cell-Kill Assay
[375] The cytotoxicity characteristics of SLT-lA::aCD20 are determined by the general cell-kill assay as described above in the previous examples using CD20+ cells. In addition, the selective cytotoxicity characteristics of SLT- lA::aCD20 are determined by the same general cell-kill assay using CD20- cells as a comparison to the CD20+ cells. The CD50 of the cytotoxic protein of this example is approximately 0.01-100 nM for CD20+ cells depending on the cell line. The CD50 of the cytotoxic protein is approximately 10-10,000 fold greater (less cytotoxic) for cells not expressing CD20 on a cellular surface as compared to cells which do express CD20 on a cellular surface.
Determining Reductions in Antigenicity and/or Immunogenicity
[376] The relative de-immunization of SLT- 1 A: :aCD20 is determined in relation to a wild-type Shiga toxin effector region polypeptide using western analyses, ELISA analyses, and murine models as described in Examples 4 and 6.
Determining the In Vivo Effects of the Cytotoxic Protein SLT-lA::aCD20 using Animal Models
[377] Animal models are used to determine the in vivo effects of the cytotoxic protein SLT-lA::aCD20 on neoplastic cells. Various mice strains are used to test the effect of the cytotoxic protein after intravenous administration on xenograft tumors in mice resulting from the injection into those mice of human neoplastic cells which express CD20 on their cell surfaces. Example 8. A Cytotoxic Protein Comprising a De-Immunized Shiga Toxin Effector Polypeptide and a Binding Region Specific to HER2 ("aHER2- VHH fused with SLT-1A")
[378] In this example, the Shiga toxin effector region was derived from the A subunit of Shiga-like Toxin 1 (SLT-1A) and comprising one or more de- immunizing amino acid substitutions described in the previous examples. The immunoglobulin-type binding region is aHER2 VHH derived from a single- domain variable region of the camelid antibody (VHH) protein 5F7, as described in U.S. Patent Application Publication 201 1/0059090. Construction, Production, and Purification of the Cytotoxic Protein "otHER2- VHH fused with SLT- 1 A"
[379] The immunoglobulin-type binding region and Shiga toxin effector region are linked together to form a fused protein (see, e.g., SEQ ID NOs: 57, 58, and 59). In this example, a polynucleotide encoding the (XHER2-VHH variable region derived from protein 5F7 may be cloned in frame with a polynucleotide encoding a linker known in the art and in frame with a polynucleotide encoding the Shiga toxin effector region comprising amino acids of SEQ ID NOs:4-52. Variants of "(XHER2-VHH fused with SLT-IA" cytotoxic proteins are created such that the binding region is optionally located adjacent to the amino-terminus of the Shiga toxin effector region and optionally comprises a carboxy -terminal endoplasmic reticulum signal motif of the KDEL family. Expression of the "(XHER2-VHH fused with SLT-IA" cytotoxic protein variants is accomplished using either bacterial and/or cell-free, protein translation systems as described in the previous examples.
Determining the In Vitro Characteristics of the Cytotoxic Protein "aHER2-VHH fused with SLT-IA"
[380] The binding characteristics of the cytotoxic protein of this example for HER2+ cells and HER2- cells is determined by a fluorescence-based, flow- cytometry assay. The Bmax for "(XHER2-VHH fused with SLT-IA" variants to HER2+ cells is measured to be approximately 50,000-200,000 MFI with a KD within the range of 0.01-100 nM, whereas there is no significant binding to HER2- cells in this assay.
[381] The ribosome inactivation abilities of the "(XHER2-VHH fused with SLT- IA" cytotoxic proteins are determined in a cell-free, in vitro protein translation as described above in the previous examples. The inhibitory effect of the cytotoxic protein of this example on cell-free protein synthesis is significant. The IC50 of "(XHER2-VHH fused with SLT-IA" variants on protein synthesis in this cell-free assay is approximately 0.1-100 pM.
Determining the Cytotoxicity of the Cytotoxic Protein "otHER2-VHH fused with SLT-IA" Using a HER2+ Cell-Kill Assay
[382] The cytotoxicity characteristics of "(XHER2-VHH fused with SLT-IA" variants are determined by the general cell-kill assay as described above in the previous examples using HER2+ cells. In addition, the selective cytotoxicity characteristics of "(XHER2-VHH fused with SLT-IA" are determined by the same general cell-kill assay using HER2- cells as a comparison to the HER2+ cells. The CD50 of the cytotoxic protein of this example is approximately 0.01-100 nM for HER2+ cells depending on the cell line. The CD50 of the cytotoxic protein is approximately 10-10,000 fold greater (less cytotoxic) for cells not expressing HER2 on a cellular surface as compared to cells which do express HER2 on a cellular surface.
Determining Reductions in Antigenicity and/or Immunogenicity
[383] The relative de-immunization of (XHER2-VHH fused with SLT-1A is determined in relation to a wild-type Shiga toxin effector region polypeptide using western analyses, ELISA analyses, and murine models as described in Examples 4 and 6.
Determining the In Vivo Effects of the Cytotoxic Protein (XHER2-VHH fused with SLT-1A Using Animal Models
[384] Animal models are used to determine the in vivo effects of the cytotoxic protein (XHER2-VHH fused with SLT-1 A on neoplastic cells. Various mice strains are used to test the effect of the cytotoxic protein after intravenous administration on xenograft tumors in mice resulting from the injection into those mice of human neoplastic cells which express HER2 on their cell surfaces. Example 9. A Cytotoxic Protein Comprising a De-Immunized Shiga Toxin Effector Polypeptide and a Binding Region Derived from the Antibody aEpstein-Barr-Antigen
[385] In this example, the Shiga toxin effector region is a de-immunzied Shiga toxin effector polypeptide derived from the A subunit of Shiga-like Toxin 1 (SLT-1 A) and comprising one or more de-immunizing amino acid substitutions described in the previous examples. An immunoglobulin-type binding region aEpstein-Barr-antigen is derived from a monoclonal antibody against an Epstein Barr antigen (Fang C et al, J Immunol Methods 287: 21-30 (2004)), which comprises an immunoglobulin-type binding region capable of binding a human cell infected by the Epstein-Barr virus or a transformed cell expressing an Epstein-Barr antigen. The Epstein-Barr antigen is expressed on multiple cell types, such as cells infected by an Epstein-Barr virus and cancer cells (e.g. lymphoma and naspharnygeal cancer cells). In addition, Epstein-Barr infection is associated with other diseases, e.g., multiple sclerosis. Construction, Production, and Purification of the Cytotoxic Protein SLT- 1 A: :otEpsteinBarr: :KDEL
[386] The immunoglobulin-type binding region aEpstein-Barr-antigen and Shiga toxin effector region are linked together, and a carboxy -terminal KDEL is added to form a protein. For example, a fusion protein is produced by expressing a polynucleotide encoding the aEpstein-Barr-antigen-binding protein SLT-lA::aEpsteinBarr::KDEL. Expression of the SLT- lA::aEpsteinBarr::KDEL cytotoxic protein is accomplished using either bacterial and/or cell-free, protein translation systems as described in the previous examples.
Determining the In Vitro Characteristics of the Cytotoxic Protein SLT- 1 A: :aEpsteinBarr: :KDEL
[387] The binding characteristics of the cytotoxic protein of this example for Epstein-Barr antigen positive cells and Epstein-Barr antigen negative cells is determined by a fluorescence-based, flow-cytometry assay. The Bmax for SLT- lA::aEpsteinBarr::KDEL to Epstein-Barr antigen positive cells is measured to be approximately 50,000-200,000 MFI with a KD within the range of 0.01- 100 nM, whereas there is no significant binding to Epstein-Barr antigen negative cells in this assay.
[388] The ribosome inactivation abilities of the SLT-lA::aEpsteinBarr::KDEL cytotoxic protein is determined in a cell-free, in vitro protein translation as described above in the previous examples. The inhibitory effect of the cytotoxic protein of this example on cell-free protein synthesis is significant. The ICso of SLT-lA::aEpsteinBarr::KDEL on protein synthesis in this cell-free assay is approximately 0.1 -100 pM.
Determining the Cytotoxicity of the Cytotoxic Protein SLT- lA::aEpsteinBarr::KDEL Using a Cell-Kill Assay
[389] The cytotoxicity characteristics of SLT-lA: :aEpsteinBarr::KDEL are determined by the general cell-kill assay as described above in the previous examples using Epstein-Barr antigen positive cells. In addition, the selective cytotoxicity characteristics of SLT-lA::aEpsteinBarr::KDEL are determined by the same general cell-kill assay using Epstein-Barr antigen negative cells as a
-iso- comparison to the Epstein-Barr antigen positive cells. The CD50 of the cytotoxic protein of this example is approximately 0.01-100 nM for Epstein-Barr antigen positive cells depending on the cell line. The CD50 of the cytotoxic protein is approximately 10-10,000 fold greater (less cytotoxic) for cells not expressing the Epstein-Barr antigen on a cellular surface as compared to cells which do express the Epstein-Barr antigen on a cellular surface.
Determining Reductions in Antigenicity and/or Immunogenicity
[390] The relative de-immunization of SLT- 1 A: :aEpsteinBarr: :KDEL is determined in relation to a wild-type Shiga toxin effector region polypeptide using western analyses, ELISA analyses, and murine models as described in Examples 4 and 6.
Determining the In Vivo Effects of the Cytotoxic Protein SLT- lA::aEpsteinBarr::KDEL using Animal Models
[391] Animal models are used to determine the in vivo effects of the cytotoxic protein SLT-lA::aEpsteinBarr::KDEL on neoplastic cells. Various mice strains are used to test the effect of the cytotoxic protein after intravenous
administration on xenograft tumors in mice resulting from the injection into those mice of human neoplastic cells which express Epstein-Barr antigens on their cell surfaces.
Example 10. A Cytotoxic Protein Comprising a De-Immunized Shiga Toxin Effector Polypeptide and a Binding Region Derived from the Antibody aLeishmania-Antigen
[392] In this example, the Shiga toxin effector region is a de-immunized Shiga toxin effector polypeptide derived from the A subunit of Shiga-like Toxin 1 (SLT-1A) and comprising one or more de-immunizing amino acid substitutions described in the previous examples. An immunoglobulin-type binding region aLeishmania-antigen is derived from an antibody generated, using techniques known in the art, to a cell-surface Leishmania antigen present on human cells harboring an intracellular trypanosomatid protozoa (see Silveira T et al, Int J Parasitol 31 : 1451-8 (2001); Kenner J et al, J Cutan Pathol 26: 130-6 (1999); Berman J and Dwyer, Clin Exp Immunol 44: 342-348 (1981)). Construction, Production, and Purification of the Cytotoxic Protein SLT- 1 A : : gLeishmania: : KDEL
[393] The immunoglobulin-type binding region a-Leishmania-antigen and Shiga toxin effector region are linked together, and a carboxy -terminal KDEL is added to form a protein. For example, a fusion protein is produced by expressing a polynucleotide encoding the Leishmania-antigen-binding protein SLT-lA::aLeishmania::KDEL. Expression of the SLT- lA::aLeishmania::KDEL cytotoxic protein is accomplished using either bacterial and/or cell-free, protein translation systems as described in the previous examples.
Determining the In Vitro Characteristics of the Cytotoxic Protein SLT- 1 A : : gLeishmania: : KDEL
[394] The binding characteristics of the cytotoxic protein of this example for Leishmania antigen positive cells and Leishmania antigen negative cells is determined by a fluorescence-based, flow-cytometry. The Bmax for SLT- lA::aLeishmania::KDEL to Leishmania antigen positive cells is measured to be approximately 50,000-200,000 MFI with a KD within the range of 0.01 - 100 nM, whereas there is no significant binding to Leishmania antigen negative cells in this assay.
[395] The ribosome inactivation abilities of the SLT-lA::aLeishmania::KDEL cytotoxic protein is determined in a cell-free, in vitro protein translation as described above in the previous examples. The inhibitory effect of the cytotoxic protein of this example on cell-free protein synthesis is significant. The ICso of SLT-lA::aLeishmania: :KDEL on protein synthesis in this cell-free assay is approximately 0.1 -100 pM.
Determining the Cytotoxicity of the Cytotoxic Protein SLT- lA::aLeishmania::KDEL Using a Cell-Kill Assay
[396] The cytotoxicity characteristics of SLT-lA::aLeishmania::KDEL are determined by the general cell-kill assay as described above in the previous examples using Leishmania antigen positive cells. In addition, the selective cytotoxicity characteristics of SLT-lA::aLeishmania::KDEL are determined by the same general cell-kill assay using Leishmania antigen negative cells as a comparison to the Leishmania antigen positive cells. The CD50 of the cytotoxic protein of this example is approximately 0.01-100 nM for Leishmania antigen positive cells depending on the cell line. The CD50 of the cytotoxic protein is approximately 10-10,000 fold greater (less cytotoxic) for cells not expressing the Leishmania antigen on a cellular surface as compared to cells which do express the Leishmania antigen on a cellular surface.
Determining Reductions in Antigenicity and/or Immunogenicity
[397] The relative de-immunization of SLT-lA::aLeishmania: :KDEL is determined in relation to a wild-type Shiga toxin effector region polypeptide using western analyses, ELISA analyses, and murine models as described in Examples 4 and 6.
Example 11. A Cytotoxic Protein Comprising a De-Immunized Shiga Toxin Effector Polypeptide and a Binding Region Derived from an
Immunoglobulin-Type Binding Region aNeurotensin-Receptor
[398] In this example, the Shiga toxin effector region is a de-immunized Shiga toxin effector polypeptide derived from the A subunit of Shiga-like Toxin 1 (SLT-1A) and comprising one or more de-immunizing amino acid substitutions described in the previous examples. An immunoglobulin-type binding region aNeurotensin-Receptor is derived from the DARPin™ (GenBank Accession: 2P2C_R) or a monoclonal antibody (Ovigne J et al, Neuropeptides 32: 247-56 (1998)) which binds the human neurotensin receptor. The neurotensin receptor is expressed by various cancer cells, such as breast cancer, colon cancer, lung cancer, melanoma, and pancreatic cancer cells.
Construction, Production, and Purification of the Cytotoxic Protein SLT- 1 A: :aNeurotensinR: :KDEL
[399] The immunoglobulin-type binding region aNeurotensinR and Shiga toxin effector region are linked together, and a carboxy -terminal KDEL is added to form a protein. For example, a fusion protein is produced by expressing a polynucleotide encoding the neurotensin-receptor-binding protein SLT- lA::aNeurotensinR::KDEL. Expression of the SLT-lA::aNeurotensinR::KDEL cytotoxic protein is accomplished using either bacterial and/or cell-free, protein translation systems as described in the previous examples.
Determining the In Vitro Characteristics of the Cytotoxic Protein SLT- 1 A: :aNeurotensinR: :KDEL
[400] The binding characteristics of the cytotoxic protein of this example for neurotensin receptor positive cells and neurotensin receptor negative cells is determined by a fluorescence-based, flow-cytometry. The Bmax for SLT- lA: :aNeurotensinR: :KDEL to neurotensin receptor positive cells is measured to be approximately 50,000-200,000 MFI with a KD within the range of 0.01 - 100 nM, whereas there is no significant binding to neurotensin receptor negative cells in this assay.
[401 ] The ribosome inactivation abilities of the SLT- lA: :aNeurotensinR: :KDEL cytotoxic protein is determined in a cell- free, in vitro protein translation as described above in the previous examples. The inhibitory effect of the cytotoxic protein of this example on cell-free protein synthesis is significant. The ICso of SLT-lA: :aNeurotensinR: :KDEL on protein synthesis in this cell-free assay is approximately 0. 1 - 100 pM. Determining the Cytotoxicity of the Cytotoxic Protein SLT- lA: :aNeurotensinR: :KDEL Using a Cell-Kill Assay
[402] The cytotoxicity characteristics of SLT- 1 A: :aNeurotensinR: :KDEL are determined by the general cell-kill assay as described above in the previous examples using neurotensin receptor positive cells. In addition, the selective cytotoxicity characteristics of SLT- 1 A: :aNeurotensinR: :KDEL are determined by the same general cell-kill assay using neurotensin receptor negative cells as a comparison to the neurotensin receptor positive cells. The CD50 of the cytotoxic protein of this example is approximately 0.01 - 100 nM for neurotensin receptor positive cells depending on the cell line. The CD50 of the cytotoxic protein is approximately 10- 10,000 fold greater (less cytotoxic) for cells not expressing neurotensin receptor on a cellular surface as compared to cells which do express neurotensin receptor on a cellular surface. Determining Reductions in Antigenicity and/or Immunogenicity
[403] The relative de-immunization of SLT-lA::aNeurotensinR::KDEL is determined in relation to a wild-type Shiga toxin effector region polypeptide using western analyses, ELISA analyses, and murine models as described in Examples 4 and 6.
Determining the In Vivo Effects of the Cytotoxic Protein SLT- IA: :aNeurotensinR::KD EL using Animal Models
[404] Animal models are used to determine the in vivo effects of the cytotoxic protein SLT-lA::aNeurotensinR::KDEL on neoplastic cells. Various mice strains are used to test the effect of the cytotoxic protein after intravenous administration on xenograft tumors in mice resulting from the injection into those mice of human neoplastic cells which express neurotensin receptors on their cell surfaces.
Example 12. A Cytotoxic Protein Comprising a De-Immunized Shiga Toxin Effector Polypeptide and a Binding Region Derived from an
Immunoglobulin-Type Binding Region aEGFR
[405] In this example, the Shiga toxin effector region is a de-immunized Shiga toxin effector polypeptide derived from the A subunit of Shiga-like Toxin 1
(SLT-IA) and comprising one or more de-immunizing amino acid substitutions described in the previous examples. The binding region aEGFR is derived from the AdNectin™ (GenBank Accession: 3QWQ_B), the Affibody™ (GenBank Accession: 2KZI_A; U.S. patent 8,598, 113), or an antibody, all of which bind one or more human epidermal growth factor receptors. The expression of epidermal growth factor receptors are associated with human cancer cells, such as, e.g., lung cancer cells, breast cancer cells, and colon cancer cells.
Construction. Production, and Purification of the Cytotoxic Protein SLT- lA::aEGFR::KDEL
[406] The immunoglobulin-type binding region aEGFR and Shiga toxin effector region are linked together, and a carboxy -terminal KDEL is added to form a protein. For example, a fusion protein is produced by expressing a polynucleotide encoding the EGFR binding protein SLT-lA::aEGFR::KDEL. Expression of the SLT- lA: :aEGFR: :KDEL cytotoxic protein is accomplished using either bacterial and/or cell-free, protein translation systems as described in the previous examples. Determining the In Vitro Characteristics of the Cytotoxic Protein SLT- lA: :otEGFR: :KDEL
[407] The binding characteristics of the cytotoxic protein of this example for EGFR+ cells and EGFR- cells is determined by a fluorescence-based, flow- cytometry. The Bmax for SLT-lA: :aEGFR::KDEL to EGFR+ cells is measured to be approximately 50,000-200,000 MFI with a KD within the range of 0.01 - 100 nM, whereas there is no significant binding to EGFR- cells in this assay.
[408] The ribosome inactivation abilities of the SLT- 1 A: :aEGFR: :KDEL cytotoxic protein is determined in a cell-free, in vitro protein translation as described above in the previous examples. The inhibitory effect of the cytotoxic protein of this example on cell-free protein synthesis is significant. The ICso of SLT- lA: :aEGFR: :KDEL on protein synthesis in this cell-free assay is approximately 0. 1 - 100 pM.
Determining the Cytotoxicity of the Cytotoxic Protein SLT- lA: :aEGFR: :KDEL Using a Cell-Kill Assay
[409] The cytotoxicity characteristics of SLT- 1 A: :aEGFR: :KDEL are determined by the general cell-kill assay as described above in the previous examples using EGFR+ cells. In addition, the selective cytotoxicity
characteristics of SLT- lA: :aEGFR: :KDEL are determined by the same general cell-kill assay using EGFR- cells as a comparison to the Leishmania antigen positive cells. The CD50 of the cytotoxic protein of this example is
approximately 0.01 - 100 nM for EGFR+ cells depending on the cell line. The CD50 of the cytotoxic protein is approximately 10- 10,000 fold greater (less cytotoxic) for cells not expressing EGFR on a cellular surface as compared to cells which do express EGFR on a cellular surface. Determining Reductions in Antigenicity and/or Immunogenicity
[410] The relative de-immunization of SLT-lA::aEGFR::KDEL is determined in relation to a wild-type Shiga toxin effector region polypeptide using western analyses, ELISA analyses, and murine models as described in Examples 4 and 6.
Determining the In Vivo Effects of the Cytotoxic Protein SLT- lA::aEGFR::KDEL using Animal Models
[41 1] Animal models are used to determine the in vivo effects of the cytotoxic protein SLT-lA::aEGFR::KDEL on neoplastic cells. Various mice strains are used to test the effect of the cytotoxic protein after intravenous administration on xenograft tumors in mice resulting from the injection into those mice of human neoplastic cells which express EGFR(s) on their cell surfaces.
Example 13. A Cytotoxic Protein Comprising a De-Immunized Shiga Toxin Effector Polypeptide and a Binding Region Derived from the Antibody aCCR5
[412] In this example, the Shiga toxin effector region is a de-immunized Shiga toxin effector polypeptide derived from the A subunit of Shiga-like Toxin 1 (SLT-1A) and comprising one or more de-immunizing amino acid substitutions described in the previous examples. An immunoglobulin-type binding region aCCR5 is derived from a monoclonal antibody against human CCR5 (CD 195) (Bernstone L et al., Hybridoma 31 : 7-19 (2012)). CCR5 is predominantly expressed on T-cells, macrophages, dendritic cells, and microglia. In addition, CCR5 plays a role in the pathogenesis and spread of the Human
Immunodeficiency Virus (HIV).
Construction, Production, and Purification of the Cytotoxic Protein SLT- lA::aCCR5::KDEL
[413] The immunoglobulin-type binding region aCCR5 and Shiga toxin effector region are linked together, and a carboxy -terminal KDEL is added to form a protein. For example, a fusion protein is produced by expressing a polynucleotide encoding the aCCR5-binding protein SLT-lA::aCCR5: :KDEL. Expression of the SLT-lA::aCCR5::KDEL cytotoxic protein is accomplished using either bacterial and/or cell-free, protein translation systems as described in the previous examples. Determining the In Vitro Characteristics of the Cytotoxic Protein SLT- lA::otCCR5
[414] The binding characteristics of the cytotoxic protein of this example for CCR5+ cells and CCR5- cells is determined by a fluorescence-based, flow- cytometry. The Bmax for SLT- 1 A: :aCCR5 : :KDEL to CCR5+ positive cells is measured to be approximately 50,000-200,000 MFI with a KD within the range of 0.01-100 nM, whereas there is no significant binding to CCR5- cells in this assay.
[415] The ribosome inactivation abilities of the SLT-lA::aCCR5::KDEL cytotoxic protein is determined in a cell-free, in vitro protein translation as described above in the previous examples. The inhibitory effect of the cytotoxic protein of this example on cell-free protein synthesis is significant. The ICso of SLT-lA::aCCR5::KDEL on protein synthesis in this cell-free assay is approximately 0.1-100 pM.
Determining the Cytotoxicity of the Cytotoxic Protein SLT-lA::aCCR5: :KDEL Using a Cell-Kill Assay
[416] The cytotoxicity characteristics of SLT-lA::aCCR5::KDEL are determined by the general cell-kill assay as described above in the previous examples using CCR5+ cells. In addition, the selective cytotoxicity
characteristics of SLT-lA::aCCR5::KDEL are determined by the same general cell-kill assay using CCR5- cells as a comparison to the CCR5+ cells. The CD50 of the cytotoxic protein of this example is approximately 0.01-100 nM for CCR5+ cells depending on the cell line. The CD50 of the cytotoxic protein is approximately 10-10,000 fold greater (less cytotoxic) for cells not expressing CCR5 on a cellular surface as compared to cells which do express CCR5 on a cellular surface.
Determining Reductions in Antigenicity and/or Immunogenicity
[417] The relative de-immunization of SLT-lA::aCCR5::KDEL is determined in relation to a wild-type Shiga toxin effector region polypeptide using western analyses, ELISA analyses, and murine models as described in Examples 4 and 6. Determining the In Vivo Effects of the Cytotoxic Protein SLT- lA::otCCR5::KDEL using Animal Models
[418] Animal models are used to determine the in vivo effects of the cytotoxic protein SLT-lA::aCCR5::KDEL on depleting T-cells from donor materials (see Tsirigotis P et al, Immunotherapy 4: 407-24 (2012)). Non-human primates are used to determine in vivo effects of SLT-lA::aCCR5. Graft versus host disease is analyzed in rhesus macaques after kidney transplantation when the donated organs are pretreated with SLT-lA::aCCR5::KDEL (see Weaver T et al, Nat Med 15: 746-9 (2009)). In vivo depletion of peripheral blood T lymphocytes in cynomolgus primates is observed after parenteral administration of different doses of SLT-lA::aCCR5::KDEL. The use of SLT-lA::aCCR5::KDEL to block HIV infection is tested by giving an acute dose of SLT- lA::aCCR5::KDEL to non-human primates in order to severely deplete circulating T-cells upon exposure to a simian immunodeficiency virus (SIV) (see Sellier P et al, PLoS One 5: el0570 (2010)).
Example 14. A Cytotoxic Protein Comprising a De-Immunized Shiga Toxin Effector Polypeptide and a Binding Region Derived from an Anti-Env Immunoglubulin Domain
[419] In this example, the Shiga toxin effector region is a de-immunized Shiga toxin effector polypeptide derived from the A subunit of Shiga toxin (StxA) and comprising one or more de-immunizing amino acid substitutions described in the previous examples. An immunoglobulin-type binding region aEnv is derived from existing antibodies that bind HIV envelope glycoprotein (Env), such as GP41, GP120, GP140, or GP160 (see e.g. Chen W et al, JMol Bio 382: 779-89 (2008); Chen W et al, Expert Opin Biol Ther 13: 657-71 (2013); van den Kerkhof T et al, Retrovirology 10: 102 (2013)) or from antibodies generated using standard techniques (see Prabakaran et al, Front Microbiol 3: 277 (2012)). Envs are HIV surface proteins that are also displayed on the cell surfaces of HIV-infected cells during HIV replication. Although Envs are expressed in infected cells predominantly in endosomal compartments, sufficient amounts of Envs could be present on a cell surface to be targeted by a highly potent cytotoxic protein of the invention. In addition, Env-targeting cytotoxic proteins might bind HIV virions and enter newly infected cells during the fusion of virions with a host cell.
[420] Because HIV displays a high rate of mutation, it is preferable to use an immunoglobulin domain that binds a functional constrained part of an Env, such as shown by broadly neutralizing antibodies that bind Envs from multiple strains of HIV (van den Kerkhof T et al, Retrovirology 10: 102 (2013)). Because the Envs present on an infected cell's surface are believed to present sterically restricted epitopes (Chen W et al, J Virol 88: 1 125-39 (2014)), it is preferable to use smaller than 100 kD and ideally smaller than 25 kD, such as sdAbs or VHH domains.
Construction, Production, and Purification of the Cytotoxic Protein SLT- lA::otEnv::KDEL
[421] The immunoglobulin-type binding region aEnv and Shiga toxin effector region are linked together, and a carboxy -terminal KDEL is added to form a cytotoxic protein. For example, a fusion protein is produced by expressing a polynucleotide encoding the αΕην-binding protein SLT-lA::aEnv::KDEL. Expression of the SLT-lA::aEnv::KDEL cytotoxic protein is accomplished using either bacterial and/or cell-free, protein translation systems as described in the previous examples.
Determining the In Vitro Characteristics of the Cytotoxic Protein SLT- lA::aEnv::KDEL
[422] The binding characteristics of the cytotoxic protein of this example for Env+ cells and Env- cells is determined by a fluorescence-based, flow- cytometry. The Bmax for SLT-lA::aEnv::KDEL to Env+ positive cells is measured to be approximately 50,000-200,000 MFI with a KD within the range of 0.01-100 nM, whereas there is no significant binding to Env- cells in this assay.
[423] The ribosome inactivation abilities of the SLT-lA::aEnv::KDEL cytotoxic protein is determined in a cell-free, in vitro protein translation as described above in the previous examples. The inhibitory effect of the cytotoxic protein of this example on cell-free protein synthesis is significant. The IC50 of SLT-lA::aEnv: :KDEL on protein synthesis in this cell- free assay is
approximately 0.1-100 pM.
Determining the Cytotoxicity of the Cytotoxic Protein SLT-lA::aEnv::KDEL Using a Cell-Kill Assay
[424] The cytotoxicity characteristics of SLT- 1 A: :aEnv: :KDEL are determined by the general cell-kill assay as described above in the previous examples using Env+ cells. In addition, the selective cytotoxicity characteristics of SLT- lA::aEnv::KDEL are determined by the same general cell-kill assay using Env- cells as a comparison to the Env+ cells. The CD50 of the cytotoxic protein of this example is approximately 0.01-100 nM for Env+ cells depending on the cell line and/or the HIV strain used to infect the cells to make them Env+. The CD50 of the cytotoxic protein is approximately 10-10,000 fold greater (less cytotoxic) for cells not expressing Env on a cellular surface as compared to cells which do express Env on a cellular surface.
Determining Reductions in Antigenicity and/or Immunogenicity
[425] The relative de-immunization of SLT-lA::aEnv::KDEL is determined in relation to a wild-type Shiga toxin effector region polypeptide using western analyses, ELISA analyses, and murine models as described in Examples 4 and 6.
Determining the In Vivo Effects of the Cytotoxic Protein SLT-lA::aEnv::KDEL using Animal Models
[426] The use of SLT- 1 A : : aEnv : : KDEL to inhibit HIV infection is tested by administering SLT-lA::aEnv::KDEL to simian immunodeficiency virus (SIV) infected non-human primates (see Sellier P et al, PLoS One 5: el0570 (2010)).
Example 15. A Cytotoxic Protein Comprising a De-Immunized Shiga Toxin Effector Polypeptide and a Binding Region Derived from the Antibody aUL18
[427] In this example, the Shiga toxin effector region is a de-immunized Shiga toxin effector polypeptide derived from the A subunit of Shiga-like Toxin 1 (SLT-1A) and comprising one or more de-immunizing amino acid substitutions described in the previous examples. An immunoglobulin-type binding region aUL18 is derived from an antibody generated, using techniques known in the art, to the cell-surface cytomegalovirus protein UL18, which is present on human cells infected with cytomegalovirus (Yang Z, Bjorkman P, Proc Natl Acad Sci USA 105: 10095-100 (2008)). The human cytomegalovirus infection is associated with various cancers and inflammatory disorders.
Construction. Production, and Purification of the Cytotoxic Protein SLT- lA::aUL18::KDEL
[428] The immunoglobulin-type binding region aUL18 and Shiga toxin effector region are linked together, and a carboxy -terminal KDEL is added to form a protein. For example, a fusion protein is produced by expressing a polynucleotide encoding the aUL18-binding protein SLT-lA::aUL18: :KDEL. Expression of the SLT-lA::aUL18::KDEL cytotoxic protein is accomplished using either bacterial and/or cell-free, protein translation systems as described in the previous examples.
Determining the In Vitro Characteristics of the Cytotoxic Protein SLT- lA::aUL18::KDEL
[429] The binding characteristics of the cytotoxic protein of this example for cytomegalovirus protein UL18 positive cells and cytomegalovirus protein UL18 negative cells is determined by a fluorescence-based, flow-cytometry. The Bmax for SLT-lA::aUL18::KDEL to cytomegalovirus protein UL18 positive cells is measured to be approximately 50,000-200,000 MFI with a KD within the range of 0.01-100 nM, whereas there is no significant binding to cytomegalovirus protein UL18 negative cells in this assay.
[430] The ribosome inactivation abilities of the SLT-lA::aUL18: :KDEL cytotoxic protein is determined in a cell-free, in vitro protein translation as described above in the previous examples. The inhibitory effect of the cytotoxic protein of this example on cell-free protein synthesis is significant. The ICso of SLT-lA::aUL18::KDEL on protein synthesis in this cell-free assay is approximately 0.1-100 pM. Determining the Cytotoxicity of the Cytotoxic Protein SLT-lA::otUL18::KDEL Using a Cell-Kill Assay
[431] The cytotoxicity characteristics of SLT-lA::aUL18::KDEL are determined by the general cell-kill assay as described above in the previous examples using cytomegalovirus protein UL18 positive cells. In addition, the selective cytotoxicity characteristics of SLT-lA::aUL18::KDEL are determined by the same general cell-kill assay using cytomegalovirus protein UL18 negative cells as a comparison to the cytomegalovirus protein UL18 positive cells. The CD50 of the cytotoxic protein of this example is approximately 0.01-100 nM for cytomegalovirus protein UL18 positive cells depending on the cell line. The CD50 of the cytotoxic protein is approximately 10-10,000 fold greater (less cytotoxic) for cells not expressing the cytomegalovirus protein UL18 on a cellular surface as compared to cells which do express the cytomegalovirus protein UL18 on a cellular surface.
Determining Reductions in Antigenicity and/or Immunogenicity
[432] The relative de-immunization of SLT-lA::aUL18::KDEL is determined in relation to a wild-type Shiga toxin effector region polypeptide using western analyses, ELISA analyses, and murine models as described in Examples 4 and 6.
Example 16. De-Immunized Cytotoxic Proteins Targeting Various Cell Types
[433] In this example, the Shiga toxin effector region is a de-immunized Shiga toxin effector polypeptide derived from the A subunit of Shiga-like Toxin 1 (SLT-1A), Shiga toxin (StxA), and/or Shiga-like Toxin 2 (SLT-2A) with any combination of B-cell epitope regions disrupted. A binding region is derived from the immunoglobulin domain from the molecule chosen from column 1 of Table 12 and which binds the extracellular target biomolecule indicated in column 2 of Table 12. The exemplary cytotoxic proteins of this example are optionally created with a carboxy-terminal KDEL-type signal motif and/or detection promoting agent(s) using reagents and techniques known in the art. The exemplary cytotoxic proteins of this example are tested as described in the previous examples using cells expressing the appropriate extracellular target biomolecules. The exemplary proteins of this example may be used, e.g., to diagnose and treat diseases, conditions, and/or disorders indicated in column 3 of Table 12.
Table 12. Various Binding Regions for Cell Targeting of Cytotoxic Proteins
Figure imgf000166_0001
and B-cell related
immune disorders, such as autoimmune disorders ipilimumab CD 152 T-cell related disorders and various cancers, such as leukemia, melanoma muromonab CD3 prevention of organ
transplant rejections natalizumab integrin a4 autoimmune disorders, such as multiple sclerosis and Crohn's disease obinutuzumab CD20 B-cell cancers, such as lymphoma and leukemia, and B-cell related immune disorders, such as autoimmune disorders ocaratuzumab CD20 B-cell cancers, such as lymphoma and leukemia, and B-cell related immune disorders, such as autoimmune disorders ocrelizumab CD20 B-cell cancers, such as lymphoma and leukemia, and B-cell related immune disorders, such as autoimmune disorders ofatumumab CD20 B-cell cancers, such as lymphoma and leukemia, and B-cell related immune disorders, such as autoimmune disorders palivizumab F protein of respiratory treat respiratory syncytial syncytial virus virus
panitumumab EGFR various cancers, such as colorectal cancer and head and neck cancer pertuzumab HER2/neu various cancers and tumors, such as breast cancer and colorectal cancer
pro 140 CCR5 HIV infection and T-cell disorders
ramucirumab VEGFR2 various cancers and
cancer related disorders, such as solid tumors rituximab CD20 B-cell cancers, such as lymphoma and leukemia, and B-cell related immune disorders, such as autoimmune disorders
Figure imgf000168_0001
mmunoogy : -
Figure imgf000169_0001
al, BMC Cancer 6: 4
Figure imgf000170_0001
fezakinumab IL-22 various cancers and immune disorders, such as rheumatoid arthritis, psoriasis
ganitumab IGF-I various cancers golimumab TNF-a various cancers and immune disorders, such as rheumatoid arthritis, psoriatic arthritis, ankylosing spondylitis infliximab TNF-a various cancers and immune disorders, such as rheumatoid arthritis, ankylosing spondylitis, psoriatic arthritis, psoriasis, Crohn's disease, ulcerative colitis ixekizumab IL-17A various cancers and immune disorders, such as autoimmune diseases mepolizumab IL-5 various immune
disorders and cancers, such as B-cell cancers nerelimomab TNF-a various cancers and immune disorders olokizumab IL6 various cancers and immune disorders ozoralizumab TNF-a inflammation perakizumab IL17A various cancers and immune disorders, such as arthritis
placulumab human TNF various immune
disorders and cancers sarilumab IL6 various cancers and immune disorders, such as rheumatoid arthritis, ankylosing spondylitis siltuximab IL-6 various cancers and immune disorders sirukumab IL-6 various cancers and immune disorders, such as rheumatoid arthritis tabalumab BAFF B-cell cancers ticilimumab or CTLA-4 various cancers tremelimumab
tildrakizumab IL23 immunologically
mediated inflammatory disorders
tnx-650 IL-13 various cancers and immune disorders, such
Figure imgf000172_0001
[434] While some embodiments of the invention have been described by way of illustration, it will be apparent that the invention can be put into practice with many modifications, variations and adaptations, and with the use of numerous equivalents or alternative solutions that are within the scope of persons skilled in the art, without departing from the spirit of the invention or exceeding the scope of the claims.
[435] All publications, patents, and patent applications are herein incorporated by reference in their entirety to the same extent as if each individual publication, patent or patent application was specifically and individually indicated to be incorporated by reference in its entirety. The disclosures of U.S. provisional patent application serial numbers 61/777, 130, 61/932,000, 61/951, 110,
61/951, 121, 62/010,918 and 62/049,325 are each incorporated herein by reference in their entirety. The disclosures of international PCT patent application serial numbers PCT/US2014/023198 and PCT/US2014/023231 are each incorporated herein by reference in their entirety. The complete disclosures of all electronically available biological sequence information from GenBank (National Center for Biotechnology Information, U.S.) for amino acid and nucleotide sequences cited herein are each incorporated herein by reference in their entirety.

Claims

The invention is claimed as follows:
A polypeptide comprising a Shiga toxin effector region comprising an amino acid sequence derived from an A Subunit of a member of the Shiga toxin Family, the Shiga toxin effector region comprising a disruption of at least one epitope region of the Shiga toxin A Subunit amino acid sequence selected from the group consisting of:
94-115 of SEQ ID NO:l, SEQ ID NO :2, or SEQ ID NO:3; 141-153 of SEQ ID NO: l or
SEQ ID NO:2; 140-156 of SEQ ID NO:3; 179-190 of SEQ ID NO: l or SEQ ID NO:2;
179-191 of SEQ ID NO:3; 204 of SEQ ID NO:3; 205 of SEQ ID NO: l or SEQ ID NO:2; and 210-218 of SEQ ID NO:3;
wherein the Shiga toxin effector region is capable of exhibiting a Shiga toxin effector function.
A polypeptide comprising a Shiga toxin effector region comprising an amino acid sequence derived from an A Subunit of a member of the Shiga toxin Family, the Shiga toxin effector region comprising a disruption of at least one epitope region of the Shiga toxin A Subunit amino acid sequence selected from the group consisting of:
1-15 of SEQ ID NO: l or SEQ ID NO:2; 3-14 of SEQ ID NO:3; 26-37 of SEQ ID NO:3;
27-37 of SEQ ID NO: 1 or SEQ ID NO:2; 39-48 of SEQ ID NO: 1 or SEQ ID NO:2; 42-
48 of SEQ ID NO:3; and 53-66 of SEQ ID NO:l, SEQ ID NO:2, or SEQ ID NO:3;
wherein the Shiga toxin effector region is capable of exhibiting a Shiga toxin effector function; and
wherein the disruption is not an amino terminal truncation of sequences that overlap with part or all of at least one disrupted epitope region.
A polypeptide comprising a Shiga toxin effector region comprising an amino acid sequence derived from an A Subunit of a member of the Shiga toxin Family, the Shiga toxin effector region comprising a disruption of at least one epitope region of the Shiga toxin A Subunit amino acid sequence selected from the group consisting of: 240-260 of SEQ ID NO:3; 243-257 of SEQ ID NO: l or SEQ ID NO:2; 254-268 of SEQ ID NO: l or SEQ ID NO:2; 262-278 of SEQ ID NO:3; 281-297 of SEQ ID NO:3; and 285-293 of SEQ ID NO: l or SEQ ID NO:2;
wherein the Shiga toxin effector region is capable of exhibiting a Shiga toxin effector function; and
wherein the disruption is not a carboxy terminal truncation of sequences that overlap with part or all of at least one disrupted epitope region.
4. The polypeptide of any one of claims 1, 2, or 3, wherein the disruption comprises a deletion of at least one amino acid within the epitope region.
5. The polypeptide of any one of claims 1, 2, or 3, wherein the disruption comprises an
insertion of at least one amino acid within the epitope region. 6. The polypeptide of any one of claims 1, 2, or 3, wherein the disruption comprises an
inversion of amino acids, wherein at least one inverted amino acid is within the epitope region.
7. The polypeptide of any one of claims 1, 2, or 3, wherein the disruption comprises a mutation.
8. The polypeptide of claim 7, wherein the disruption comprises an amino acid residue
substitution within the epitope region.
9. The polypeptide of claim 8, wherein the substitution is selected from the group consisting of:
D to A, D to G, D to V, D to L, D to I, D to F, D to S, D to Q, E to A, E to G, E to V, E to
L, E to I, E to F, E to S, E to Q, E to N, E to D, E to M, E to R, G to A, H to A, H to G, H to V, H to L, H to I, H to F, H to M, K to A, K to G, K to V, K to L, K to I, K to M, K to H, N to A, N to G, N to V, N to L, N to I, N to F, P to A, P to G, P to F, R to A, R to G, R to V, R to L, R to I, R to F, R to M, R to Q, R to S, R to K, R to H, S to A, S to G, S to V, S to L, S to I, S to F, S to M, T to A, T to G, T to V, T to L, T to I, T to F, T to M, T to S,
Y to A, Y to G, Y to V, Y to L, Y to I, Y to F, and Y to M.
10. The polypeptide of claim 9, wherein an amino acid residue substitution occurs at the natively positioned amino acid selected from the group consisting of amino acid:
1 of SEQ ID NO : 1 or SEQ ID NO :2; 4 of SEQ ID NO : 1 , SEQ ID NO :2, or SEQ ID NO:3; 8 of SEQ ID NO:l, SEQ ID NO:2, or SEQ ID NO:3; 9 of SEQ ID NO:l, SEQ ID NO:2, or SEQ ID NO:3; 11 of SEQ ID NO:l, SEQ ID NO:2, or SEQ ID NO:3; 33 of
SEQ ID NO: 1 or SEQ ID NO:2; 43 of SEQ ID NO: 1 or SEQ ID NO:2; 45 of SEQ ID NO: 1 or SEQ ID NO:2; 47 of SEQ ID NO: 1 or SEQ ID NO:2; 48 of SEQ ID NO: 1 , SEQ ID NO:2, or SEQ ID NO:3; 49 of SEQ ID NO: 1 or SEQ ID NO:2; 53 of SEQ ID NO: 1 or SEQ ID NO:2; 55 of SEQ ID NO:l or SEQ ID NO:2; 58 of SEQ ID NO:l, SEQ ID NO:2, or SEQ ID NO:3; 59 of SEQ ID NO:l, SEQ ID NO:2, or SEQ ID NO:3; 60 of
SEQ ID NO : 1 or SEQ ID NO :2; 61 of SEQ ID NO : 1 or SEQ ID NO :2; 62 of SEQ ID NO:l or SEQ ID NO:2; 94 of SEQ ID NO:l, SEQ ID NO:2, or SEQ ID NO :3; 96 of SEQ IDNO:l, SEQ IDNO:2, or SEQ IDNO:3; 109 of SEQ IDNO:l, SEQ IDNO:2, or SEQ IDNO:3; HOofSEQ IDNO:l or SEQ IDNO:2; 112 of SEQ IDNO:l, SEQ IDNO:2, orSEQIDNO:3; SE 147 of SEQ ID NO:l, SEQ ID NO:2, or SEQ ID NO:3; 179 of SEQ
IDNO:l, SEQ IDNO:2, or SEQ IDNO:3; 180 of SEQ IDNO:l or SEQ IDNO:2; 181 of SEQ ID NO:l or SEQ ID NO:2; 183 of SEQ ID NO:l, SEQ ID NO:2, or SEQ ID NO:3; 184 of SEQ IDNO:l, SEQ IDNO:2, or SEQ IDNO:3; 185 of SEQ IDNO:l or SEQ IDNO:2; 186 of SEQ IDNO:l, SEQ IDNO:2, or SEQ IDNO:3; 187 of SEQ ID NO:l orSEQIDNO:2; 188 of SEQ ID NO: 1 orSEQIDNO:2; 189 of SEQ ID NO:l or
SEQ ID NO:2; 204 of SEQ ID NO:3; 205 of SEQ ID NO: 1 or SEQ ID NO:2; 247 of SEQ ID NO: 1 or SEQ ID NO:2; 247 of SEQ ID NO:3; 248 of SEQ ID NO: 1 or SEQ ID NO:2; 250 of SEQ ID NO:3;251 of SEQ ID NO:l or SEQ ID NO:2; 264 of SEQ IDNO:l, SEQ ID NO:2, or SEQ ID NO:3; 265 of SEQ ID NO:l or SEQ ID NO:2; and 286 of SEQ ID NO:l orSEQIDNO:2.
11. The polypeptide of claim 10, wherein the substitution is to an amino acid which is a member of the conservative amino acid and at a position selected from the group consisting of:
Kl to A, G, V, L, I, F, M and H; T4 to A, G, V, L, I, F, M, and S; S8 to A, G, V, I, L, F, and M; T9 to A, G, V, I, L, F, M, and S; S9 to A, G, V, L, I, F, and M; Kl 1 to A, G, V, L,
I, F, M and H; S33 to A, G, V, L, I, F, and M; S45 to A, G, V, L, I, F, and M; T45 to A, G, V, L, I, F, and M; D47 to A, G, V, L, I, F, S, and Q; N48 to A, G, V, L, and M; L49 to A or G; D53 to A, G, V, L, I, F, S, and Q; R55 to A, G, V, L, I, F, M, Q, S, K, and H; D58 to A, G, V, L, I, F, S, and Q; P59 to A, G, and F; E60 to A, G, V, L, I, F, S, Q, N, D, M, and R; E61 to A, G, V, L, I, F, S, Q, N, D, M, and R; G62 to A; D94 to A, G, V, L, I, F, S, and Q; S96 to A, G, V, I, L, F, and M; SI 09 to A, G, V, I, L, F, and M; T109 to A,
G, V, I, L, F, M, and S; G110 to A; SI 12 to A, G, V, L, I, F, and M; G147 to A; R179 to A, G, V, L, I, F, M, Q, S, K, and H; T180 to A, G, V, L, I, F, M, and S; T181 to A, G, V, L, I, F, M, and S; D183 to A, G, V, L, I, F, S, and Q; D184 to A, G, V, L, I, F, S, and Q; SI 86 to A, G, V, I, L, F, and M; G187 to A; R188 to A, G, V, L, I, F, M, Q, S, K, and H; S 189 to A, G, V, I, L, F, and M; R204 to A, G, V, L, I, F, M, Q, S, K, and H; R205 to A,
G, V, L, I, F, M, Q, S, K and H; S247 to A, G, V, I, L, F, and M; Y247 to A, G, V, L, I, F, and M; R248 to A, G, V, L, I, F, M, Q, S, K, and H; R250 to A, G, V, L, I, F, M, Q, S, K, and H; R251 to A, G, V, L, I, F, M, Q, S, K, and H; D264 to A, G, V, L, I, F, S, and Q; G264 to A; and T286 to A, G, V, L, I, F, M, and S.
12. The polypeptide of any one of claims 1-11, wherein the Shiga toxin effector region is derived from amino acids 75 to 251 of SEQ ID NO: l, SEQ ID NO:2, or SEQ ID NO:3.
13. The polypeptide of any one of claims 1-11, wherein the Shiga toxin effector region is derived from amino acids 1 to 241 of SEQ ID NO: l, SEQ ID NO:2, or SEQ ID NO:3.
14. The polypeptide of claim 13, wherein the Shiga toxin effector region is derived from amino acids 1 to 251 of SEQ ID NO: l, SEQ ID NO:2, or SEQ ID NO:3. 15. The polypeptide of claim 14, wherein the Shiga toxin effector region is derived from amino acids 1 to 261 of SEQ ID NO: l, SEQ ID NO:2, or SEQ ID NO:3.
16. The polypeptide of claim 14, wherein the Shiga toxin effector region comprises or consists essentially of SEQ ID NOs: 4-52.
17. A protein comprising
a) a Shiga toxin effector region comprising the polypeptide of any one of claims 1-16 and b) a binding region comprising one or more polypeptides and capable of specifically binding at least one extracellular target biomolecule.
18. The protein of claim 17, wherein the binding region comprises a polypeptide selected from the group consisting of:
complementary determining region 3 fragment, constrained FR3-CDR3-FR4 polypeptide, single-domain antibody fragment, single-chain variable fragment, antibody variable fragment, antigen-binding fragment, Fd fragment, fibronection-derived 10th fibronectin type III domain, tenacsin type III domain, ankyrin repeat motif domain, low-density- lipoprotein-receptor-derived A-domain, lipocalin, Kunitz domain, Protein- A-derived Z domain, gamma-B crystalline-derived domain, ubiquitin-derived domain, Sac7d-derived polypeptide, Fyn-derived SH2 domain, miniprotein, C-type lectin-like domain scaffold, engineered antibody mimic, and any genetically manipulated counterparts of any of the foregoing that retain binding functionality.
19. The cytotoxic protein of claim 17 or 18, whereby upon administration of the cytotoxic
protein to a cell physically coupled with an extracellular target biomolecule of said binding region, the cytotoxic protein is capable of causing death of said cell.
20. The cytotoxic protein of claim 19, whereby upon administration of the cytotoxic protein to a first populations of cells whose members are physically coupled to extracellular target biomolecules of said binding region, and a second population of cells whose members are not physically coupled to any extracellular target biomolecule of said binding region, the cytotoxic effect of the cytotoxic protein to members of said first population of cells relative to members of said second population of cells is at least 3 -fold greater.
21. The protein of any one of claims 17-20, wherein the binding region is capable of binding to an extracellular target biomolecule selected from the group consisting of: CD20, CD22, CD40, CD79, CD25, CD30, HER2/neu/ErbB2, EGFR, EpCAM, EphB2, prostate-specific membrane antigen, Cripto, endoglin, fibroblast activated protein, Lewis- Y, CD19, CD21, CS1/ SLAMF7, CD33, CD52, EpCAM, CEA, gpA33, Mucins, TAG- 72, carbonic anhydrase IX, folate binding protein, ganglioside GD2, ganglioside GD3, ganglioside GM2, ganglioside Lewis-Y2, VEGFR, Alpha Vbeta3, Alpha5betal,
ErbBl/EGFR, Erb3, c-MET, IGF1R, EphA3, TRAIL-R1, TRAIL-R2, RANKL, FAP, Tenascin, CD64, mesothelin, BRCA1, MART-l/MelanA, gplOO, tyrosinase, TRP-1, TRP-2, MAGE-1, MAGE-3, GAGE-1/2, BAGE, RAGE, NY-ESO-1, CDK-4, beta- catenin, MUM-1, caspase-8, KIAA0205, HPVE6, SART-1, PRAME, carcinoembryonic antigen, prostate specific antigen, prostate stem cell antigen, human aspartyl
(asparaginyl) beta-hydroxylase, EphA2, HER3/ErbB-3, MUC1, MART-l/MelanA, gplOO, tyrosinase associated antigen, HPV-E7, Epstein-Barr Virus antigens, Bcr-Abl, alpha-fetoprotein antigen, 17-A1, bladder tumor antigen, CD38, CD15, CD23, CD52, CD53, CD88, CD129, CD183, CD191, CD193, CD244, CD294, CD305, C3AR, FceRIa, galectin-9, mrp-14, siglec-8, siglec-10, CD49d, CD13, CD44, CD54, CD63, CD69, CD123, CD193, TLR4, FceRIa, IgE, CD107a, CD203c, CD14, CD15, CD33, CD64, CD68, CD80, CD86, CD105, CD115, F4/80, ILT-3, Galectin-3, CDl la-c, GITRL, MHC Class II, CD284-TLR4, CD107-Mac3, CD195-CCR5, HLA-DR, CD16/32, CD282- TLR2, CD1 lc, CD 123, and any immunogenic fragment of any of the foregoing.
The protein of any one of claims 17-21 further comprising a carboxy-terminal endoplasmic reticulum retention/retrieval signal motif of a member of the KDEL family.
The protein of claim 22 further comprising the carboxy-terminal endoplasmic reticulum retention/retrieval signal motif selected from the group consisting of:
KDEL, HDEF, HDEL, RDEF, RDEL, WDEL, YDEL, HEEF, HEEL, KEEL, REEL, KAEL, KCEL, KFEL, KGEL, KHEL, KLEL, KNEL, KQEL, KREL, KSEL, KVEL, KWEL, KYEL, KEDL, KIEL, DKEL, FDEL, KDEF, KKEL, HADL, HAEL, HIEL, HNEL, HTEL, KTEL, HVEL, NDEL, QDEL, REDL, RNEL, RTDL, RTEL, SDEL, TDEL, and SKEL.
24. The protein of any one of claims 17-23, wherein the binding region and the Shiga toxin effector region are physically oriented within the protein such that the binding region is not located proximally to the amino-terminus of the Shiga toxin effector region. 25. The protein of any one of claims 17-24 comprising or consisting essentially of any one of SEQ ID NO:53, SEQ ID NO:54, SEQ ID NO:55, SEQ ID NO:56, SEQ ID NO:57, SEQ ID NO:58, or SEQ ID NO:59.
26. The protein of any one of claims 17-25, wherein the Shiga toxin effector region comprises a mutation relative to a naturally occurring A Subunit of a member of the Shiga toxin family which changes the enzymatic activity of the Shiga toxin effector region, the mutation selected from at least one amino acid residue deletion or substitution.
27. The protein of claim 26, wherein the mutation reduces or eliminates cytotoxicity.
28. A pharmaceutical composition comprising the polypeptide or protein of any one of claims 1- 27 and at least one pharmaceutically acceptable excipient or carrier.
29. A polynucleotide capable of encoding the polypeptide or protein of any one of claims 1-27, or a complement thereof, or a fragment of any of the foregoing.
30. An expression vector comprising the polynucleotide of claim 29.
31. A host cell comprising any one of the polynucleotides or expression vectors of claims 29-30.
32. A method of killing a cell comprising the step of contacting the cell with the polypeptide or protein of any one of claims 1-27 or the pharmaceutical composition of claim 28.
33. The method of claim 32, wherein the contacting occurs in vitro.
34. The method of claim 32, wherein the contacting occurs in vivo.
35. A method of treating a disease, disorder, or condition in a patient comprising the step of administering to a patient in need thereof a therapeutically effective amount of the polypeptide or protein of any one of claims 1-27 or the pharmaceutical composition of claim 28.
36. The method of claim 35, wherein the disease, disorder, or condition is selected from the group consisting of: cancer, tumor, immune disorder, and microbial infection.
37. The method of claim 36, wherein the cancer selected from the group consisting of:
bone cancer, breast cancer, central/peripheral nervous system cancer, gastrointestinal cancer, germ cell cancer, glandular cancer, head-neck cancer, hematological cancer, kidney-urinary tract cancer, liver cancer, lung/pleura cancer, prostate cancer, sarcoma, skin cancer, and uterine cancer. 38. The method of claim 36, wherein the immune disorder associated is with a disease selected from the group consisting of:
amyloidosis, ankylosing spondylitis, asthma, Crohn's disease, diabetes, graft rejection, graft-vs.-host disease, Hashimoto's thyroiditis, hemolytic uremic syndrome, HIV-related diseases, lupus erythematosus, multiple sclerosis, polyarteritis, psoriasis, psoriatic arthritis, rheumatoid arthritis, scleroderma, septic shock, Sjorgren's syndrome, ulcerative colitis, and vasculitis.
39. A composition comprising the polypeptide or protein of any one of claims 1-27 for the
treatment or prevention of a cancer, tumor, immune disorder, or microbial infection.
40. Use of the composition of matter of any one of claims 1-31 in the manufacture of a
medicament for the treatment or prevention of a cancer, tumor, immune disorder, or microbial infection.
41. A diagnostic composition comprising
the protein of any one of claims 17-27 and
a detection promoting agent. 42. Use of the composition of matter of any one of claims 1-31 or 41 in the diagnosis, prognosis, or characterization of a disease, disorder, or condition.
43. A method of detecting a cell comprising the steps of:
contacting the cell with the diagnostic composition of claim 41 and
detecting the presence of the diagnostic composition.
44. The method of claim 43, wherein the contacting occurs in vitro.
45. The method of claim 43, wherein the contacting occurs in vivo.
46. The method of claim 43, wherein the detecting occurs in vitro.
47. The method of claim 43, wherein the detecting occurs in vivo. 48. Use of the polypeptide of any one of claims 1-16 as a component of an immunogen for
immunization and/or vaccination of a mammal.
49. A kit comprising the composition of matter of any one of claims 1-31 or 41, and an
additional reagent and/or pharmaceutical delivery device.
PCT/US2015/012970 2014-01-27 2015-01-26 De-immunized shiga toxin a subunit effector polypeptides for applications in mammals WO2015113007A1 (en)

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US15/114,487 US20160340394A1 (en) 2014-01-27 2015-01-26 De-immunized shiga toxin a subunit effector polypeptides for applications in mammals
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MX2016009809A MX2016009809A (en) 2014-01-27 2015-01-26 De-immunized shiga toxin a subunit effector polypeptides for applications in mammals.
CN201580015672.2A CN106414483A (en) 2014-01-27 2015-01-26 De-immunized shiga toxin A subunit effector polypeptides for applications in mammals
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ES15704153T ES2749862T3 (en) 2014-01-27 2015-01-26 Shiga toxin A subunit deimmunized effector polypeptides for mammalian applications
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AU2015209065A AU2015209065C1 (en) 2014-01-27 2015-01-26 De-immunized Shiga toxin A Subunit effector polypeptides for applications in mammals
ES18207811T ES2919749T3 (en) 2014-06-11 2015-06-10 Molecules targeting cytotoxic cells resistant to cleavage by protease
US15/317,892 US10815469B2 (en) 2014-06-11 2015-06-10 Cell-targeting molecules comprising protease-cleavage resistant, Shiga toxin A subunit effector polypeptides and carboxy-terminal moieties
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US14/965,882 US20160177284A1 (en) 2014-01-27 2015-12-10 Cell-targeted molecules comprising amino-terminus proximal or amino-terminal shiga toxin a subunit effector regions
IL246632A IL246632B (en) 2014-01-27 2016-07-06 De-immunized shiga toxin a subunit effector polypeptides for applications in mammals
US15/747,501 US20210138076A2 (en) 2014-01-27 2016-07-25 Cell-targeting molecules comprising shiga toxin a subunit effectors and cd8+ t-cell epitopes
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US16/013,600 US20180291359A1 (en) 2014-01-27 2018-06-20 Cell-targeting molecules comprising amino-terminus proximal or amino-terminal, shiga toxin a subunit effector regions
AU2019204364A AU2019204364C1 (en) 2014-01-27 2019-06-21 De-immunized Shiga toxin A subunit effector polypeptides for applications in mammals
AU2019240612A AU2019240612B2 (en) 2014-06-11 2019-10-02 Protease-cleavage resistant, Shiga toxin A Subunit effector polypeptides and cell-targeted molecules comprising the same
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US17/030,657 US20210017512A1 (en) 2014-06-11 2020-09-24 Cell-targeting molecules comprising protease-cleavage resistant, shiga toxin a subunit effector polypeptides and carboxy-terminal moieties
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US17/345,576 US12065469B2 (en) 2014-01-27 2021-06-11 De-immunized Shiga toxin a subunit effector polypeptides for applications in mammals
US17/459,133 US20220401568A1 (en) 2014-01-27 2021-08-27 Cell-targeting molecules comprising shiga toxin a subunit effectors and cd8+ t-cell epitopes
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